From 429ec1481257a796e8831c1a7ccea420c9123a03 Mon Sep 17 00:00:00 2001 From: percyfal Date: Tue, 19 Dec 2023 08:55:32 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20NBISwede?= =?UTF-8?q?n/genecovr@c5fcd375a416c771b0cc7fe93355313d31ee66c8=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/genecovr.html | 37 ++++++----- ...gbc-plot-depth-by-breadth-by-contigs-1.png | Bin 42805 -> 43453 bytes index.html | 62 ++++++++++++++++-- pkgdown.yml | 2 +- reference/readPsl.html | 2 +- search.json | 2 +- 6 files changed, 77 insertions(+), 28 deletions(-) diff --git a/articles/genecovr.html b/articles/genecovr.html index f6bfb40..1c54ae3 100644 --- a/articles/genecovr.html +++ b/articles/genecovr.html @@ -106,14 +106,14 @@

On object repr

genecovr has functionality to read pairwise sequence alignment files and converts the pairwise alignments to -AlignmentPairs objects. An AlignmentPairs -object is a subclass of the Bioconductor class -S4Vectors::Pairs. A Pairs object in turn +genecovr::AlignmentPairs objects. An +AlignmentPairs object is a subclass of the Bioconductor +class S4Vectors::Pairs. A Pairs object in turn aligns two vectors along slot names first and second, and the AlignmentPairs object adds slots for the query and subject, and possibly extra slots related to additional information in the alignment file. The query and subject are -GRanges objects or objects derived from the +GenomicRanges::GRanges objects or objects derived from the GRangesclass.

@@ -127,10 +127,11 @@

Analysing gene body coverageGenomeInfoDb::Seqinfo objects that can be used to set +sequence information on the parsed output. We load the fasta indices and +parse the psl files with genecovr::readPsl, storing the +results in an genecovr::AlignmentPairsList for +convenience.

 assembly_fai_fn <- list(
   nonpol = system.file("extdata", "nonpolished.fai",
@@ -186,7 +187,7 @@ 
Plot ratio matches to
 
Plot summary indel and match distributions
 

 
We can also select multiple columns to plot in the
-AlignmentPairsList.

+genecovr::AlignmentPairsList.

 
 cnames <- c("misMatches", "query.NumInsert", "query.BaseInsert")
 plot(apl, aes(x = id, y = get_expr(enquo(cnames))), which = "violin") +
@@ -204,10 +205,10 @@ 
Plot summary indel and match
 

 
Plot number of indels
 

-
The function insertionSummary summarizes the number of
-insertions, either at the transcript level (default) or per alignment.
-The intuition is that as assembly quality improves, the number of indels
-go down.

+
The function genecovr::insertionSummary summarizes the
+number of insertions, either at the transcript level (default) or per
+alignment. The intuition is that as assembly quality improves, the
+number of indels go down.

 
First we show a plot with the number of insertions per alignment. A
 consequence of this is that as a transcript may be split in multiple
 alignments, the bars are of unequal height.

@@ -232,15 +233,15 @@ 
Plot number of indels
 
Gene body coverage
 

-
The function geneBodyCoverage takes an
+
The function genecovr::geneBodyCoverage takes an
 AlignmentPairs object and summarizes breadth of coverage
 and number of subject hits per transcript.

 
 gbc <- lapply(apl, geneBodyCoverage, min.match = 0.1)

 
A summary can be obtained with the
-summarizeGeneBodyCoverage function. We define a range of
-minimum match hit cutoffs to filter out hits with too few matches in the
-aligned region.

+genecovr::summarizeGeneBodyCoverage function. We define a
+range of minimum match hit cutoffs to filter out hits with too few
+matches in the aligned region.

 
 min.match <- c(0.25, 0.5, 0.75, 0.9)
 names(min.match) <- min.match
@@ -273,7 +274,7 @@ 
Number of contigs per transcript
 
A fragmented assembly will lead to more transcripts mapping to
 several contigs. We calculate the number of subjects by coverage cutoff
-with the function countSubjectsByCoverage

+with the function genecovr::countSubjectsByCoverage

 
 data <- dplyr::bind_rows(
   lapply(
diff --git a/articles/genecovr_files/figure-html/gbc-plot-depth-by-breadth-by-contigs-1.png b/articles/genecovr_files/figure-html/gbc-plot-depth-by-breadth-by-contigs-1.png
index 5edb7d0fc1b6429ee4e1ba62b612b23d37f5c84e..8e57022fd666579781375ed73263357a3e8ac148 100644
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diff --git a/index.html b/index.html
index 286b133..02a2162 100644
--- a/index.html
+++ b/index.html
@@ -61,18 +61,22 @@
 
    • 
 
 
-
    Perform gene body coverage analyses in R to evaluate genome assembly quality.
    
+
    genecovr is an R package that provides plotting functions that summarize gene transcript to genome alignments. The main purpose is to assess the effect of polishing and scaffolding operations has on the quality of a genome assembly. The gene transcript set is a large sequence set consisting of assembled transcripts from RNA-seq data generated in relation to a genome assembly project. Therefore, genecovr serves as a complement to software such as BUSCO, which evaluates genome assembly quality using a smaller set of well-defined single-copy orthologs.
    
 
    
 
    Installation
 
    
 
    You can install the released version of genecovr from NBIS GitHub with:
    
 
    -# install.packages("devtools")
+# If necessary, uncomment to install devtools
+# install.packages("devtools")
 devtools::install_github("NBISweden/genecovr")
    
 
    
 
    
-
    Quick usage
+
    Usage
 
    
+
    
+
    genecovr script quick start
+
    
 
    There is a helper script for generating basic plots located in PACKAGE_DIR/bin/genecovr. Create a data input csv-delimited file with columns
    
 
      
 
    1. data label
      2. 
@@ -82,11 +86,55 @@ 
      Quick usagePACKAGE_DIR/bin/genecovr indata.csv
    
+
    
+
    Example
+
    
+
    There are example files located in PACKAGE_DIR/inst/extdata consisting of two psl alignment files containing gmap alignments and fasta indices for the transcript sequences and two for different assembly versions:
    
+
      
+
    • nonpolished.fai - fasta index for raw assembly
      • 
+
    • polished.fai - fasta index for polished assembly
      • 
+
    • transcripts.fai - fasta index for transcript sequences
      • 
+
    • transcripts2nonpolished.psl - gmap alignments, transcripts to raw assembly
      • 
+
    • transcripts2polished.psl - gmap alignments, transcripts to polished assembly
      • 
+
    
+
    Using these files and the labels non and pol for the different assemblies, a genecovr input file (called e.g., assemblies.csv) would look as follows:
    
+
    nonpol,transcripts2nonpolished.psl,nonpolished.fai,transcripts.fai
+pol,transcripts2polished.psl,polished.fai,transcripts.fai
    
+
    and the command to run would be:
    
+
    genecovr assemblies.csv
    
+
    
+
    
+
    genecovr options
+
    
+
    To list genecovr script options, type ’genecovr -h`:
    
+
    usage: genecovr [-h] [-v] [-p number]
+                             [-d OUTPUT_DIRECTORY] [--height HEIGHT]
+                             [--width WIDTH]
+                             csvfile
+
+positional arguments:
+  csvfile               csv-delimited file with columns
+                            1. data label
+                            2. mapping file (supported formats: psl)
+                            3. assembly file (fasta or fasta index)
+                            4. transcript file (fasta or fasta index)
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -v, --verbose         print extra output
+  -p number, --cpus number
+                        number of cpus [default 1]
+  -d OUTPUT_DIRECTORY, --output-directory OUTPUT_DIRECTORY
+                        output directory
+  --height HEIGHT       figure height in inches [default 6.0]
+  --width WIDTH         figure width in inches [default 6.0]
    
+
    
+
    
+
    
+
    R package vignette
+
    
+
    Alternatively, import the library in an R script and use the package functions. See Get started or run vignette("genecovr") for a minimum working example.
    
 
    
-
    
-
    Vignette
-
    
-
    Alternatively, import the library as usual in an R script and use the package functions. See the vignette for a minimum working example.
    diff --git a/search.json b/search.json index ee5a4de..8320773 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"path":"https://nbisweden.github.io/genecovr/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://nbisweden.github.io/genecovr/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://nbisweden.github.io/genecovr/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":" Copyright (C) 2020 Per Unneberg This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . genecovr Copyright (C) 2020 Per Unneberg This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"about","dir":"Articles","previous_headings":"","what":"About","title":"Gene body coverage analysis in R","text":"vignette describes analyses gene body coverage genome assembly evaluation metrics R using genecovr package. genecovr contains functionality parsing alignment files, calculating gene body coverages, generating simple QC metrics assess assembly quality output. start example analysis, describe genecovr represents pairwise alignments.","code":""},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"r-setup","dir":"Articles","previous_headings":"About","what":"R setup","title":"Gene body coverage analysis in R","text":"","code":"library(genecovr) library(ggplot2) library(S4Vectors) library(tidyr) library(rlang) library(viridis) library(RColorBrewer) bw <- theme_bw(base_size = 18) %+replace% theme(axis.text.x = element_text(angle = 45, hjust = 1, vjust = 1)) theme_set(bw) color_pal_4 <- brewer.pal(name = \"Paired\", n = 4) psize <- 3"},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"on-object-representation-of-pairwise-sequence-alignments","dir":"Articles","previous_headings":"About","what":"On object representation of pairwise sequence alignments","title":"Gene body coverage analysis in R","text":"genecovr functionality read pairwise sequence alignment files converts pairwise alignments AlignmentPairs objects. AlignmentPairs object subclass Bioconductor class S4Vectors::Pairs. Pairs object turn aligns two vectors along slot names first second, AlignmentPairs object adds slots query subject, possibly extra slots related additional information alignment file. query subject GRanges objects objects derived GRangesclass.","code":""},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"analysing-gene-body-coverage","dir":"Articles","previous_headings":"","what":"Analysing gene body coverage","title":"Gene body coverage analysis in R","text":"section analyse mapping transcriptome non-polished polished assembly. mapping results consist two gmap files psl format, transcripts2nonpolished.psl transcripts2polished.psl. addition fasta index files assemblies (nonpolished.fai polished.fai) transcriptome (transcripts.fai). fasta indices used generate Seqinfo objects can used set sequence information parsed output. load fasta indices parse psl files readPsl, storing results AlignmentPairsList convenience.","code":"assembly_fai_fn <- list( nonpol = system.file(\"extdata\", \"nonpolished.fai\", package = \"genecovr\" ), pol = system.file(\"extdata\", \"polished.fai\", package = \"genecovr\" ) ) transcripts_fai_fn <- list( nonpol = system.file(\"extdata\", \"transcripts.fai\", package = \"genecovr\" ), pol = system.file(\"extdata\", \"transcripts.fai\", package = \"genecovr\" ) ) assembly_sinfo <- endoapply(assembly_fai_fn, readFastaIndex) transcripts_sinfo <- endoapply(transcripts_fai_fn, readFastaIndex) psl_fn <- list( nonpol = system.file(\"extdata\", \"transcripts2nonpolished.psl\", package = \"genecovr\" ), pol = system.file(\"extdata\", \"transcripts2polished.psl\", package = \"genecovr\" ) ) apl <- AlignmentPairsList( lapply(names(psl_fn), function(x) { readPsl(psl_fn[[x]], seqinfo.sbjct = assembly_sinfo[[x]], seqinfo.query = transcripts_sinfo[[x]] ) }) ) names(apl) <- names(psl_fn)"},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"plot-ratio-matches-to-width-of-alignment-regions","dir":"Articles","previous_headings":"Analysing gene body coverage","what":"Plot ratio matches to width of alignment regions","title":"Gene body coverage analysis in R","text":"first plot ratio matches width alignments respect transcripts. clear shift higher percentage matches polished assembly, expected.","code":"plot(apl, aes(x = id, y = matches / query.width, fill = id), which = \"violin\") + ylim(0.8, 1) + scale_fill_viridis_d()"},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"plot-summary-indel-and-match-distributions","dir":"Articles","previous_headings":"Analysing gene body coverage","what":"Plot summary indel and match distributions","title":"Gene body coverage analysis in R","text":"can also select multiple columns plot AlignmentPairsList.","code":"cnames <- c(\"misMatches\", \"query.NumInsert\", \"query.BaseInsert\") plot(apl, aes(x = id, y = get_expr(enquo(cnames))), which = \"violin\") + facet_wrap(. ~ name, scales = \"free\") plot(apl, aes(x = id, y = get_expr(enquo(cnames))), which = \"boxplot\") + facet_wrap(. ~ name, scales = \"free\") plot(apl, aes(x = id, y = get_expr(enquo(cnames))), which = \"boxplot\") + facet_wrap(. ~ name, scales = \"free\") + scale_y_continuous(trans = \"log10\")"},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"plot-number-of-indels","dir":"Articles","previous_headings":"Analysing gene body coverage","what":"Plot number of indels","title":"Gene body coverage analysis in R","text":"function insertionSummary summarizes number insertions, either transcript level (default) per alignment. intuition assembly quality improves, number indels go . First show plot number insertions per alignment. consequence transcript may split multiple alignments, bars unequal height. alternative summarize number insertions transcript. Currently, consideration taken overlapping alignments, meaning insertions may counted . improvement use non-overlapping set alignments fewest number insertions.","code":"x <- insertionSummary(apl, reduce = FALSE) ggplot(x, aes(id)) + geom_bar(aes(fill = cuts)) + scale_fill_viridis_d(name = \"qNumInsert\", begin = 1, end = 0) x <- insertionSummary(apl) ggplot(x, aes(id)) + geom_bar(aes(fill = cuts)) + scale_fill_viridis_d(name = \"qNumInsert\", begin = 1, end = 0)"},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"gene-body-coverage","dir":"Articles","previous_headings":"Analysing gene body coverage","what":"Gene body coverage","title":"Gene body coverage analysis in R","text":"function geneBodyCoverage takes AlignmentPairs object summarizes breadth coverage number subject hits per transcript. summary can obtained summarizeGeneBodyCoverage function. define range minimum match hit cutoffs filter hits matches aligned region. combine data plot resulting coverages","code":"gbc <- lapply(apl, geneBodyCoverage, min.match = 0.1) min.match <- c(0.25, 0.5, 0.75, 0.9) names(min.match) <- min.match gbc_summary <- lapply(apl, function(x) { y <- do.call(\"rbind\", lapply(min.match, function(mm) { summarizeGeneBodyCoverage(x, min.match = mm) })) }) library(dplyr) data <- dplyr::bind_rows(lapply(gbc_summary, data.frame), .id = \"dataset\") h <- max(data$total) hmax <- ceiling(h / 100) * 100 ggplot( subset(data, min.match == 0.25), aes(x = min.coverage, y = count, group = dataset, color = dataset) ) + geom_abline(slope = 0, intercept = h) + geom_point(aes(shape = dataset, color = dataset), size = psize) + geom_line() + scale_color_viridis_d() + scale_y_continuous(breaks = c(pretty(data$count)), limits = c(0, hmax))"},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"number-of-contigs-per-transcript","dir":"Articles","previous_headings":"Analysing gene body coverage","what":"Number of contigs per transcript","title":"Gene body coverage analysis in R","text":"fragmented assembly lead transcripts mapping several contigs. calculate number subjects coverage cutoff function countSubjectsByCoverage plot results","code":"data <- dplyr::bind_rows( lapply( lapply(apl, countSubjectsByCoverage), data.frame ), .id = \"dataset\" ) ggplot(data = data, aes( x = factor(min.coverage), y = Freq, fill = n.subjects )) + geom_bar(stat = \"identity\", position = position_stack()) + scale_fill_viridis_d(begin = 1, end = 0) + facet_wrap(. ~ dataset, nrow = 1, labeller = label_both)"},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"duplicated-versus-split-transcripts","dir":"Articles","previous_headings":"Analysing gene body coverage","what":"Duplicated versus split transcripts","title":"Gene body coverage analysis in R","text":"Transcripts map one contig anything split contigs duplicated entirely subjects. One way investigate whether trancripts split duplicated plot depth coverage divided breadth coverage length-normalized coverage. First combine data: plot ratio depthOfCoverage / breadthOfCoverage length-normalized coverage Alternatively can make jitter plot depthOfCoverage breadthOfCoverage number subjects. similar picture obtained via histogram plot. Finally, assess whether length bias ratio condition number subjects per transcript.","code":"data <- dplyr::bind_rows( lapply( lapply(apl, geneBodyCoverage), data.frame ), .id = \"dataset\" ) ggplot(data = data, aes( x = coverage, y = depthOfCoverage / breadthOfCoverage, color = factor(n.subjects) )) + geom_point(size = psize) + scale_color_viridis_d(alpha = .8) + xlim(0, 1) + ylim(0, 5) + facet_wrap(. ~ dataset) ggplot( data = subset(data, n.subjects > 1), aes(x = factor(dataset), y = depthOfCoverage / breadthOfCoverage) ) + geom_jitter(size = psize, alpha = .6) + facet_wrap(. ~ n.subjects) ggplot( data = subset(data, n.subjects > 1), aes(depthOfCoverage / breadthOfCoverage) ) + geom_histogram() + facet_grid(vars(dataset)) ggplot( data = subset(data, n.subjects > 1), aes(x = factor(dataset), y = seqlengths) ) + geom_boxplot() + facet_grid(. ~ n.subjects)"},{"path":"https://nbisweden.github.io/genecovr/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Per Unneberg. Author, maintainer.","code":""},{"path":"https://nbisweden.github.io/genecovr/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Unneberg P (2023). genecovr: Gene body coverage analysis evaluate genome assemblies. R package version 0.1.0, https://nbisweden.github.io/genecovr/.","code":"@Manual{, title = {genecovr: Gene body coverage analysis to evaluate genome assemblies}, author = {Per Unneberg}, year = {2023}, note = {R package version 0.1.0}, url = {https://nbisweden.github.io/genecovr/}, }"},{"path":"https://nbisweden.github.io/genecovr/index.html","id":"genecovr","dir":"","previous_headings":"","what":"Gene body coverage analysis to evaluate genome assemblies","title":"Gene body coverage analysis to evaluate genome assemblies","text":"Perform gene body coverage analyses R evaluate genome assembly quality.","code":""},{"path":"https://nbisweden.github.io/genecovr/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Gene body coverage analysis to evaluate genome assemblies","text":"can install released version genecovr NBIS GitHub :","code":"# install.packages(\"devtools\") devtools::install_github(\"NBISweden/genecovr\")"},{"path":"https://nbisweden.github.io/genecovr/index.html","id":"quick-usage","dir":"","previous_headings":"","what":"Quick usage","title":"Gene body coverage analysis to evaluate genome assemblies","text":"helper script generating basic plots located PACKAGE_DIR/bin/genecovr. Create data input csv-delimited file columns data label mapping file (supported formats: psl) assembly file (fasta fasta index) transcript file (fasta fasta index) Columns 3 4 can set missing value (NA) case sequence sizes inferred alignment files. run script generate plots:","code":"PACKAGE_DIR/bin/genecovr indata.csv"},{"path":"https://nbisweden.github.io/genecovr/index.html","id":"vignette","dir":"","previous_headings":"","what":"Vignette","title":"Gene body coverage analysis to evaluate genome assemblies","text":"Alternatively, import library usual R script use package functions. See vignette minimum working example.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairs-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Representation of an alignment pair — AlignmentPairs-class","title":"Representation of an alignment pair — AlignmentPairs-class","text":"Pairs subclass Constructor AlignmentPairs","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairs-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Representation of an alignment pair — AlignmentPairs-class","text":"","code":"AlignmentPairs(query, subject, ...) # S4 method for GRanges,GRanges AlignmentPairs(query, subject, ...)"},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairs-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Representation of an alignment pair — AlignmentPairs-class","text":"query vectorized object representing query subject vectorized object representing subject ... Arguments pass constructor","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairs-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Representation of an alignment pair — AlignmentPairs-class","text":"AlignmentPairs object","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairs-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Representation of an alignment pair — AlignmentPairs-class","text":"AlignmentPairs class extends Pairs-class","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairs-class.html","id":"constructor","dir":"Reference","previous_headings":"","what":"Constructor","title":"Representation of an alignment pair — AlignmentPairs-class","text":"AlignmentPairs(query, subject, ...): Constructs AlignmentPairs object aligning vectors query subject.","code":""},{"path":[]},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairsList-class.html","id":null,"dir":"Reference","previous_headings":"","what":"List of AlignmentPairs instances — AlignmentPairsList-class","title":"List of AlignmentPairs instances — AlignmentPairsList-class","text":"Subclass S4Vectors SimpleList, entry AlignmentPairs object","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairsList-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List of AlignmentPairs instances — AlignmentPairsList-class","text":"","code":"AlignmentPairsList(obj, ...) # S4 method for list AlignmentPairsList(obj)"},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairsList-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List of AlignmentPairs instances — AlignmentPairsList-class","text":"obj list ... ellipsis","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairsList-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List of AlignmentPairs instances — AlignmentPairsList-class","text":"AlignmentPairsList object","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairsList-class.html","id":"constructor","dir":"Reference","previous_headings":"","what":"Constructor","title":"List of AlignmentPairs instances — AlignmentPairsList-class","text":"AlignmentPairsList(obj, ...): Constructs AlignmentPairsList object input","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/as.data.frame-AlignmentPairsList-method.html","id":null,"dir":"Reference","previous_headings":"","what":"as.data.frame — as.data.frame,AlignmentPairsList-method","title":"as.data.frame — as.data.frame,AlignmentPairsList-method","text":"Convert AlignmentPairsList data.frame.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/as.data.frame-AlignmentPairsList-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"as.data.frame — as.data.frame,AlignmentPairsList-method","text":"","code":"# S4 method for AlignmentPairsList as.data.frame(x, ..., .id = \"id\")"},{"path":"https://nbisweden.github.io/genecovr/reference/as.data.frame-AlignmentPairsList-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"as.data.frame — as.data.frame,AlignmentPairsList-method","text":"x AlignmentPairsList object ... additional parameters lapply .id name id column added dplyr::bind_rows","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/as.data.frame-AlignmentPairsList-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"as.data.frame — as.data.frame,AlignmentPairsList-method","text":"data.frame","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/autoplot.AlignmentPairsList.html","id":null,"dir":"Reference","previous_headings":"","what":"autoplot.AlignmentPairsList — autoplot.AlignmentPairsList","title":"autoplot.AlignmentPairsList — autoplot.AlignmentPairsList","text":"autoplot.AlignmentPairsList","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/autoplot.AlignmentPairsList.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"autoplot.AlignmentPairsList — autoplot.AlignmentPairsList","text":"","code":"# S3 method for AlignmentPairsList autoplot(object, aes, vars, ..., which = \"point\")"},{"path":"https://nbisweden.github.io/genecovr/reference/autoplot.AlignmentPairsList.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"autoplot.AlignmentPairsList — autoplot.AlignmentPairsList","text":"object AlignmentPairsList aes aes mapping vars variable mapping facet plots ... additional parameters ggplot function plot make. 'grid' option makes scatter plot marginal densities","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/breadthOfCoverage.html","id":null,"dir":"Reference","previous_headings":"","what":"breadthOfCoverage — breadthOfCoverage","title":"breadthOfCoverage — breadthOfCoverage","text":"Calculate breadth coverage sequence id","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/breadthOfCoverage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"breadthOfCoverage — breadthOfCoverage","text":"","code":"breadthOfCoverage(x)"},{"path":"https://nbisweden.github.io/genecovr/reference/breadthOfCoverage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"breadthOfCoverage — breadthOfCoverage","text":"x GRangesList object","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/breadthOfCoverage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"breadthOfCoverage — breadthOfCoverage","text":"integer representing sum range widths","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/countSubjectsByCoverage.html","id":null,"dir":"Reference","previous_headings":"","what":"countSubjectsByCoverage — countSubjectsByCoverage","title":"countSubjectsByCoverage — countSubjectsByCoverage","text":"countSubjectsByCoverage","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/countSubjectsByCoverage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"countSubjectsByCoverage — countSubjectsByCoverage","text":"","code":"countSubjectsByCoverage( x, min.coverage = seq(0.25, 1, 0.25), min.match = 0.9, nmax = 5 )"},{"path":"https://nbisweden.github.io/genecovr/reference/countSubjectsByCoverage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"countSubjectsByCoverage — countSubjectsByCoverage","text":"x AlignmentPairs DataFrame object min.coverage coverage cutoffs apply transcripts min.match filter hits fraction matching bases less min.match nmax maximum number subjects count","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/deletions-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Get deletions from an alignment. — deletions","title":"Get deletions from an alignment. — deletions","text":"Get deletions alignment.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/deletions-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get deletions from an alignment. — deletions","text":"","code":"deletions(x, ...)"},{"path":"https://nbisweden.github.io/genecovr/reference/deletions-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get deletions from an alignment. — deletions","text":"x Object representation sequence alignment ... Additional argument list","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/deletions-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get deletions from an alignment. — deletions","text":"numeric","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/divergence-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Get divergence from an alignment — divergence","title":"Get divergence from an alignment — divergence","text":"Get divergence alignment.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/divergence-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get divergence from an alignment — divergence","text":"","code":"divergence(x, ...)"},{"path":"https://nbisweden.github.io/genecovr/reference/divergence-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get divergence from an alignment — divergence","text":"x Object representation sequence alignment ... Additional argument list","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/divergence-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get divergence from an alignment — divergence","text":"numeric","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/geneBodyCoverage.html","id":null,"dir":"Reference","previous_headings":"","what":"Get gene body coverage — geneBodyCoverage","title":"Get gene body coverage — geneBodyCoverage","text":"geneBodyCoverage(obj, ...): calculate gene body coverage input Calculate geneBodyCoverage query sequences","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/geneBodyCoverage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get gene body coverage — geneBodyCoverage","text":"","code":"geneBodyCoverage(obj, ...) # S4 method for AlignmentPairs geneBodyCoverage(obj, min.match = 0.9) # S4 method for AlignmentPairsList geneBodyCoverage(obj, min.match = 0.9, bpparam = NULL)"},{"path":"https://nbisweden.github.io/genecovr/reference/geneBodyCoverage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get gene body coverage — geneBodyCoverage","text":"obj AlignmentPairs object ... additional parameters min.match filter hits fraction matching bases less min.match bpparam BiocParallel parameter object","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/geneBodyCoverage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get gene body coverage — geneBodyCoverage","text":"reduced filtered DataFrame object row transcript. See @details information seqnames seqlengths columns collected corresponding seqinfo object. breadthOfCoverage total width reduced regions transcript corresponds much transcript covered. Dividing breadthOfCoverage total transcript length gives coverage fraction. depthOfCoverage sums ranges estimate many times range present. Dividing depthOfCoverage breadthOfCoverage indicates multiplicity query. queries map multiple subjects, value close 1 indicates query split several subjects, whereas higher value indicates sequence duplication subject level.","code":"The revmap column maps the output ranges to the input ranges as lists of numerical ids. These ids can be used to retrieve the corresponding AlignmentPairs ranges providing a link to the subjects. The hitCoverage lists the width of each reduced hit, and hitStart and hitEnd provide the transcript coordinates of these hits."},{"path":"https://nbisweden.github.io/genecovr/reference/geneBodyCoverage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get gene body coverage — geneBodyCoverage","text":"Given AlignmentPairs object, calculate gene body coverages query sequences. regions. instance, one hit spans coordinates 100-400 another 200-500, merge 100-500. function calculates many overlaps merged, rationale >1 overlaps seqname, sequence associated multiple distinct regions subject sequence. Thus, unit interest query, function seeks identify reduced disjoint regions query sequence map subject.","code":"The function returns a GRanges object with reduced regions, i.e. overlaps are merged. Information about matches and mismatches is currently dropped as it usually is not possible to infer where mismatches occur. Instead, the data column `coverage` simply holds the ratio of the width of the region to the transcript length. Summing up coverages from disjoint regions then gives total coverage of the transcript. The cutoff is used to filter regions based on the ratio of matches to the width of the region. Since the association between query and subject regions is removed, the return value is a GRanges object consisting of the reduced query ranges with a revmap and coverage attribute."},{"path":"https://nbisweden.github.io/genecovr/reference/genecovr-package.html","id":null,"dir":"Reference","previous_headings":"","what":"genecovr: Gene body coverage analysis to evaluate genome assemblies — genecovr-package","title":"genecovr: Gene body coverage analysis to evaluate genome assemblies — genecovr-package","text":"Gene body coverage analysis evaluate genome assemblies.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/genecovr-package.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"genecovr: Gene body coverage analysis to evaluate genome assemblies — genecovr-package","text":"genecovr package provides functionality evaluating gene body coverage metrics genome assemblies. central measurement unit gene transcript model.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/genecovr-package.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"genecovr: Gene body coverage analysis to evaluate genome assemblies — genecovr-package","text":"autoplot: plot GRanges objects gene body coverage metrics","code":""},{"path":[]},{"path":"https://nbisweden.github.io/genecovr/reference/genecovr-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"genecovr: Gene body coverage analysis to evaluate genome assemblies — genecovr-package","text":"Maintainer: Per Unneberg per.unneberg@nbis.se (ORCID)","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/insertions-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Get insertions from an alignment — insertions","title":"Get insertions from an alignment — insertions","text":"Get insertions alignment.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/insertions-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get insertions from an alignment — insertions","text":"","code":"insertions(x, ...) # S4 method for GRanges insertions(x, as.bases = FALSE, ...)"},{"path":"https://nbisweden.github.io/genecovr/reference/insertions-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get insertions from an alignment — insertions","text":"x Object representation sequence alignment ... Additional argument list .bases Get insertions base pairs","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/insertions-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get insertions from an alignment — insertions","text":"numeric","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/matches-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"matches — matches","title":"matches — matches","text":"Get matches alignment. Get mismatches alignment. Get matches parts repeats alignment.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/matches-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matches — matches","text":"","code":"matches(x, ...) mismatches(x, ...) repmatches(x, ...) # S4 method for AlignmentPairs matches(x) # S4 method for AlignmentPairs mismatches(x) # S4 method for AlignmentPairs repmatches(x)"},{"path":"https://nbisweden.github.io/genecovr/reference/matches-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matches — matches","text":"x Object representation sequence alignment ... Additional argument list","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/matches-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matches — matches","text":"numeric numeric numeric","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/plot.AlignmentPairsList.html","id":null,"dir":"Reference","previous_headings":"","what":"plot — plot.AlignmentPairsList","title":"plot — plot.AlignmentPairsList","text":"plot AlignmentPairsList","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/plot.AlignmentPairsList.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"plot — plot.AlignmentPairsList","text":"","code":"# S3 method for AlignmentPairsList plot(x, ...)"},{"path":"https://nbisweden.github.io/genecovr/reference/plot.AlignmentPairsList.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"plot — plot.AlignmentPairsList","text":"x object plot ... additional arguments autoplot","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/psl-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"methods-psl — psl methods","title":"methods-psl — psl methods","text":"Methods dealing psl data","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/psl-methods.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"methods-psl — psl methods","text":"Methods dealing Pattern Space Layout (psl) file format. See http://genome.ucsc.edu/FAQ/FAQformat.html information.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/query-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve query from object — query","title":"Retrieve query from object — query","text":"object query slot retrieve query object. object query slot set query.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/query-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve query from object — query","text":"","code":"query(x, ...) query(x) <- value # S4 method for AlignmentPairs query(x) # S4 method for AlignmentPairs,GRanges query(x) <- value"},{"path":"https://nbisweden.github.io/genecovr/reference/query-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve query from object — query","text":"x object representing alignment ... Additional arguments value object representing query","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/query-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve query from object — query","text":"query object object representing alignment updated query slot","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/readFastaIndex.html","id":null,"dir":"Reference","previous_headings":"","what":"readFastaIndex — readFastaIndex","title":"readFastaIndex — readFastaIndex","text":"Read fasta index file","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/readFastaIndex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"readFastaIndex — readFastaIndex","text":"","code":"readFastaIndex(fai, ...)"},{"path":"https://nbisweden.github.io/genecovr/reference/readFastaIndex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"readFastaIndex — readFastaIndex","text":"fai fasta index file ... additional parameters pass GenomeInfoDb::Seqinfo","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/readFastaIndex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"readFastaIndex — readFastaIndex","text":"Seqinfo object","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/readFastaIndex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"readFastaIndex — readFastaIndex","text":"","code":"fai <- system.file(\"extdata\", \"polished.fai\", package=\"genecovr\") sinfo <- readFastaIndex(fai)"},{"path":"https://nbisweden.github.io/genecovr/reference/readPsl.html","id":null,"dir":"Reference","previous_headings":"","what":"readPsl — readPsl","title":"readPsl — readPsl","text":"Read psl output","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/readPsl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"readPsl — readPsl","text":"","code":"readPsl( filename, seqinfo.query = NULL, seqinfo.sbjct = NULL, metadata = list(), ... )"},{"path":"https://nbisweden.github.io/genecovr/reference/readPsl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"readPsl — readPsl","text":"filename input filename seqinfo.query Seqinfo object query (transcripts) seqinfo.sbjct Seqinfo object subject (reference) metadata metadata AlignmentPairs result ... additional parameters","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/readPsl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"readPsl — readPsl","text":"AlignmentPairs object","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/readPsl.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"readPsl — readPsl","text":"Parse Pattern Space Layout (psl) file; see http://genome.ucsc.edu/FAQ/FAQformat.html information psl file format","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/readPsl.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"readPsl — readPsl","text":"","code":"fn <- system.file(\"extdata\", \"transcripts2polished.psl\", package=\"genecovr\") ap <- readPsl(fn) #> reading file /home/runner/work/_temp/Library/genecovr/extdata/transcripts2polished.psl #> manually inferring seqinfo for query #> manually inferring seqinfo for subject #> Processed 239 lines in 0.081 secs"},{"path":"https://nbisweden.github.io/genecovr/reference/reduceHitCoverage.html","id":null,"dir":"Reference","previous_headings":"","what":"reduceHitCoverage — reduceHitCoverage","title":"reduceHitCoverage — reduceHitCoverage","text":"Reduce hit coverage seqname","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/reduceHitCoverage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"reduceHitCoverage — reduceHitCoverage","text":"","code":"reduceHitCoverage(x, min.match = 0.9)"},{"path":"https://nbisweden.github.io/genecovr/reference/reduceHitCoverage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"reduceHitCoverage — reduceHitCoverage","text":"x AlignmentPairs object min.match filter hits fraction matching bases less min.match","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/reduceHitCoverage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"reduceHitCoverage — reduceHitCoverage","text":"reduced filtered GRanges object","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/reduceHitCoverage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"reduceHitCoverage — reduceHitCoverage","text":"Given AlignmentPairs object, reduce overlapping query regions. instance, one hit spans coordinates 100-400 another 200-500, merge 100-500. function calculates many overlaps merged, rationale >1 overlaps seqname, sequence associated multiple distinct regions subject sequence. Thus, unit interest query, function seeks identify reduced disjoint regions query sequence map subject.","code":"The function returns a GRanges object with reduced regions, i.e. overlaps are merged. Information about matches and mismatches is currently dropped as it usually is not possible to infer where mismatches occur. Instead, the data column `coverage` simply holds the ratio of the width of the region to the transcript length. Summing up coverages from disjoint regions then gives total coverage of the transcript. The cutoff is used to filter regions based on the ratio of matches to the width of the region. Since the association between query and subject regions is removed, the return value is a GRanges object consisting of the reduced query ranges with a revmap and coverage attribute."},{"path":"https://nbisweden.github.io/genecovr/reference/reduceHitCoverage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"reduceHitCoverage — reduceHitCoverage","text":"","code":"ranges <- IRanges::IRanges( start=c(100, 200, 700), end=c(400, 500, 1000) ) qry <- GenomicRanges::GRanges( ranges=ranges, seqnames=c(\"t1\"), seqinfo=GenomeInfoDb::Seqinfo(seqnames=c(\"t1\"), seqlengths=c(1050)) ) ranges <- IRanges::IRanges( start=c(1000, 1000, 1000), end=c(1300, 1300, 1300) ) sbj <- GenomicRanges::GRanges(ranges=ranges, seqnames=c(\"c1\", \"c2\", \"c1\")) x <- AlignmentPairs(query=qry, subject=sbj, matches=c(300, 290, 280)) if (FALSE) gr <- reduceHitCoverage(x, 0.1)"},{"path":"https://nbisweden.github.io/genecovr/reference/sbjct-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve subject from object — sbjct","title":"Retrieve subject from object — sbjct","text":"object subject slot retrieve subject object. object subject slot set subject.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/sbjct-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve subject from object — sbjct","text":"","code":"sbjct(x, ...) sbjct(x) <- value # S4 method for AlignmentPairs sbjct(x) # S4 method for AlignmentPairs,GRanges sbjct(x) <- value"},{"path":"https://nbisweden.github.io/genecovr/reference/sbjct-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve subject from object — sbjct","text":"x object representing alignment ... Additional arguments value object representing subject","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/sbjct-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve subject from object — sbjct","text":"object representing subject object representing alignment updated subject slot","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/score-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve score from object — score","title":"Retrieve score from object — score","text":"object score slot retrieve score object.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/score-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve score from object — score","text":"","code":"score(x, ...)"},{"path":"https://nbisweden.github.io/genecovr/reference/score-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve score from object — score","text":"x object representing alignment ... Additional arguments","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/score-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve score from object — score","text":"numeric","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/sequence-data-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"methods-sequence-data — sequence data methods","title":"methods-sequence-data — sequence data methods","text":"Methods dealing sequence data","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/summarizeGeneBodyCoverage.html","id":null,"dir":"Reference","previous_headings":"","what":"summarizeGeneBodyCoverage — summarizeGeneBodyCoverage","title":"summarizeGeneBodyCoverage — summarizeGeneBodyCoverage","text":"summarizeGeneBodyCoverage","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/summarizeGeneBodyCoverage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"summarizeGeneBodyCoverage — summarizeGeneBodyCoverage","text":"","code":"summarizeGeneBodyCoverage(x, min.coverage = seq(0, 1, 0.05), min.match = 0.9)"},{"path":"https://nbisweden.github.io/genecovr/reference/summarizeGeneBodyCoverage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"summarizeGeneBodyCoverage — summarizeGeneBodyCoverage","text":"x AlignmentPairs DataFrame object min.coverage coverage cutoffs apply transcripts min.match filter hits fraction matching bases less min.match","code":""}] +[{"path":"https://nbisweden.github.io/genecovr/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://nbisweden.github.io/genecovr/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://nbisweden.github.io/genecovr/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":" Copyright (C) 2020 Per Unneberg This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . genecovr Copyright (C) 2020 Per Unneberg This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"about","dir":"Articles","previous_headings":"","what":"About","title":"Gene body coverage analysis in R","text":"vignette describes analyses gene body coverage genome assembly evaluation metrics R using genecovr package. genecovr contains functionality parsing alignment files, calculating gene body coverages, generating simple QC metrics assess assembly quality output. start example analysis, describe genecovr represents pairwise alignments.","code":""},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"r-setup","dir":"Articles","previous_headings":"About","what":"R setup","title":"Gene body coverage analysis in R","text":"","code":"library(genecovr) library(ggplot2) library(S4Vectors) library(tidyr) library(rlang) library(viridis) library(RColorBrewer) bw <- theme_bw(base_size = 18) %+replace% theme(axis.text.x = element_text(angle = 45, hjust = 1, vjust = 1)) theme_set(bw) color_pal_4 <- brewer.pal(name = \"Paired\", n = 4) psize <- 3"},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"on-object-representation-of-pairwise-sequence-alignments","dir":"Articles","previous_headings":"About","what":"On object representation of pairwise sequence alignments","title":"Gene body coverage analysis in R","text":"genecovr functionality read pairwise sequence alignment files converts pairwise alignments genecovr::AlignmentPairs objects. AlignmentPairs object subclass Bioconductor class S4Vectors::Pairs. Pairs object turn aligns two vectors along slot names first second, AlignmentPairs object adds slots query subject, possibly extra slots related additional information alignment file. query subject GenomicRanges::GRanges objects objects derived GRangesclass.","code":""},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"analysing-gene-body-coverage","dir":"Articles","previous_headings":"","what":"Analysing gene body coverage","title":"Gene body coverage analysis in R","text":"section analyse mapping transcriptome non-polished polished assembly. mapping results consist two gmap files psl format, transcripts2nonpolished.psl transcripts2polished.psl. addition fasta index files assemblies (nonpolished.fai polished.fai) transcriptome (transcripts.fai). fasta indices used generate GenomeInfoDb::Seqinfo objects can used set sequence information parsed output. load fasta indices parse psl files genecovr::readPsl, storing results genecovr::AlignmentPairsList convenience.","code":"assembly_fai_fn <- list( nonpol = system.file(\"extdata\", \"nonpolished.fai\", package = \"genecovr\" ), pol = system.file(\"extdata\", \"polished.fai\", package = \"genecovr\" ) ) transcripts_fai_fn <- list( nonpol = system.file(\"extdata\", \"transcripts.fai\", package = \"genecovr\" ), pol = system.file(\"extdata\", \"transcripts.fai\", package = \"genecovr\" ) ) assembly_sinfo <- endoapply(assembly_fai_fn, readFastaIndex) transcripts_sinfo <- endoapply(transcripts_fai_fn, readFastaIndex) psl_fn <- list( nonpol = system.file(\"extdata\", \"transcripts2nonpolished.psl\", package = \"genecovr\" ), pol = system.file(\"extdata\", \"transcripts2polished.psl\", package = \"genecovr\" ) ) apl <- AlignmentPairsList( lapply(names(psl_fn), function(x) { readPsl(psl_fn[[x]], seqinfo.sbjct = assembly_sinfo[[x]], seqinfo.query = transcripts_sinfo[[x]] ) }) ) names(apl) <- names(psl_fn)"},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"plot-ratio-matches-to-width-of-alignment-regions","dir":"Articles","previous_headings":"Analysing gene body coverage","what":"Plot ratio matches to width of alignment regions","title":"Gene body coverage analysis in R","text":"first plot ratio matches width alignments respect transcripts. clear shift higher percentage matches polished assembly, expected.","code":"plot(apl, aes(x = id, y = matches / query.width, fill = id), which = \"violin\") + ylim(0.8, 1) + scale_fill_viridis_d()"},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"plot-summary-indel-and-match-distributions","dir":"Articles","previous_headings":"Analysing gene body coverage","what":"Plot summary indel and match distributions","title":"Gene body coverage analysis in R","text":"can also select multiple columns plot genecovr::AlignmentPairsList.","code":"cnames <- c(\"misMatches\", \"query.NumInsert\", \"query.BaseInsert\") plot(apl, aes(x = id, y = get_expr(enquo(cnames))), which = \"violin\") + facet_wrap(. ~ name, scales = \"free\") plot(apl, aes(x = id, y = get_expr(enquo(cnames))), which = \"boxplot\") + facet_wrap(. ~ name, scales = \"free\") plot(apl, aes(x = id, y = get_expr(enquo(cnames))), which = \"boxplot\") + facet_wrap(. ~ name, scales = \"free\") + scale_y_continuous(trans = \"log10\")"},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"plot-number-of-indels","dir":"Articles","previous_headings":"Analysing gene body coverage","what":"Plot number of indels","title":"Gene body coverage analysis in R","text":"function genecovr::insertionSummary summarizes number insertions, either transcript level (default) per alignment. intuition assembly quality improves, number indels go . First show plot number insertions per alignment. consequence transcript may split multiple alignments, bars unequal height. alternative summarize number insertions transcript. Currently, consideration taken overlapping alignments, meaning insertions may counted . improvement use non-overlapping set alignments fewest number insertions.","code":"x <- insertionSummary(apl, reduce = FALSE) ggplot(x, aes(id)) + geom_bar(aes(fill = cuts)) + scale_fill_viridis_d(name = \"qNumInsert\", begin = 1, end = 0) x <- insertionSummary(apl) ggplot(x, aes(id)) + geom_bar(aes(fill = cuts)) + scale_fill_viridis_d(name = \"qNumInsert\", begin = 1, end = 0)"},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"gene-body-coverage","dir":"Articles","previous_headings":"Analysing gene body coverage","what":"Gene body coverage","title":"Gene body coverage analysis in R","text":"function genecovr::geneBodyCoverage takes AlignmentPairs object summarizes breadth coverage number subject hits per transcript. summary can obtained genecovr::summarizeGeneBodyCoverage function. define range minimum match hit cutoffs filter hits matches aligned region. combine data plot resulting coverages","code":"gbc <- lapply(apl, geneBodyCoverage, min.match = 0.1) min.match <- c(0.25, 0.5, 0.75, 0.9) names(min.match) <- min.match gbc_summary <- lapply(apl, function(x) { y <- do.call(\"rbind\", lapply(min.match, function(mm) { summarizeGeneBodyCoverage(x, min.match = mm) })) }) library(dplyr) data <- dplyr::bind_rows(lapply(gbc_summary, data.frame), .id = \"dataset\") h <- max(data$total) hmax <- ceiling(h / 100) * 100 ggplot( subset(data, min.match == 0.25), aes(x = min.coverage, y = count, group = dataset, color = dataset) ) + geom_abline(slope = 0, intercept = h) + geom_point(aes(shape = dataset, color = dataset), size = psize) + geom_line() + scale_color_viridis_d() + scale_y_continuous(breaks = c(pretty(data$count)), limits = c(0, hmax))"},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"number-of-contigs-per-transcript","dir":"Articles","previous_headings":"Analysing gene body coverage","what":"Number of contigs per transcript","title":"Gene body coverage analysis in R","text":"fragmented assembly lead transcripts mapping several contigs. calculate number subjects coverage cutoff function genecovr::countSubjectsByCoverage plot results","code":"data <- dplyr::bind_rows( lapply( lapply(apl, countSubjectsByCoverage), data.frame ), .id = \"dataset\" ) ggplot(data = data, aes( x = factor(min.coverage), y = Freq, fill = n.subjects )) + geom_bar(stat = \"identity\", position = position_stack()) + scale_fill_viridis_d(begin = 1, end = 0) + facet_wrap(. ~ dataset, nrow = 1, labeller = label_both)"},{"path":"https://nbisweden.github.io/genecovr/articles/genecovr.html","id":"duplicated-versus-split-transcripts","dir":"Articles","previous_headings":"Analysing gene body coverage","what":"Duplicated versus split transcripts","title":"Gene body coverage analysis in R","text":"Transcripts map one contig anything split contigs duplicated entirely subjects. One way investigate whether trancripts split duplicated plot depth coverage divided breadth coverage length-normalized coverage. First combine data: plot ratio depthOfCoverage / breadthOfCoverage length-normalized coverage Alternatively can make jitter plot depthOfCoverage breadthOfCoverage number subjects. similar picture obtained via histogram plot. Finally, assess whether length bias ratio condition number subjects per transcript.","code":"data <- dplyr::bind_rows( lapply( lapply(apl, geneBodyCoverage), data.frame ), .id = \"dataset\" ) ggplot(data = data, aes( x = coverage, y = depthOfCoverage / breadthOfCoverage, color = factor(n.subjects) )) + geom_point(size = psize) + scale_color_viridis_d(alpha = .8) + xlim(0, 1) + ylim(0, 5) + facet_wrap(. ~ dataset) ggplot( data = subset(data, n.subjects > 1), aes(x = factor(dataset), y = depthOfCoverage / breadthOfCoverage) ) + geom_jitter(size = psize, alpha = .6) + facet_wrap(. ~ n.subjects) ggplot( data = subset(data, n.subjects > 1), aes(depthOfCoverage / breadthOfCoverage) ) + geom_histogram() + facet_grid(vars(dataset)) ggplot( data = subset(data, n.subjects > 1), aes(x = factor(dataset), y = seqlengths) ) + geom_boxplot() + facet_grid(. ~ n.subjects)"},{"path":"https://nbisweden.github.io/genecovr/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Per Unneberg. Author, maintainer.","code":""},{"path":"https://nbisweden.github.io/genecovr/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Unneberg P (2023). genecovr: Gene body coverage analysis evaluate genome assemblies. R package version 0.1.0, https://nbisweden.github.io/genecovr/.","code":"@Manual{, title = {genecovr: Gene body coverage analysis to evaluate genome assemblies}, author = {Per Unneberg}, year = {2023}, note = {R package version 0.1.0}, url = {https://nbisweden.github.io/genecovr/}, }"},{"path":"https://nbisweden.github.io/genecovr/index.html","id":"genecovr","dir":"","previous_headings":"","what":"Gene body coverage analysis to evaluate genome assemblies","title":"Gene body coverage analysis to evaluate genome assemblies","text":"genecovr R package provides plotting functions summarize gene transcript genome alignments. main purpose assess effect polishing scaffolding operations quality genome assembly. gene transcript set large sequence set consisting assembled transcripts RNA-seq data generated relation genome assembly project. Therefore, genecovr serves complement software BUSCO, evaluates genome assembly quality using smaller set well-defined single-copy orthologs.","code":""},{"path":"https://nbisweden.github.io/genecovr/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Gene body coverage analysis to evaluate genome assemblies","text":"can install released version genecovr NBIS GitHub :","code":"# If necessary, uncomment to install devtools # install.packages(\"devtools\") devtools::install_github(\"NBISweden/genecovr\")"},{"path":[]},{"path":"https://nbisweden.github.io/genecovr/index.html","id":"genecovr-script-quick-start","dir":"","previous_headings":"Usage","what":"genecovr script quick start","title":"Gene body coverage analysis to evaluate genome assemblies","text":"helper script generating basic plots located PACKAGE_DIR/bin/genecovr. Create data input csv-delimited file columns data label mapping file (supported formats: psl) assembly file (fasta fasta index) transcript file (fasta fasta index) Columns 3 4 can set missing value (NA) case sequence sizes inferred alignment files. run script generate plots:","code":"PACKAGE_DIR/bin/genecovr indata.csv"},{"path":"https://nbisweden.github.io/genecovr/index.html","id":"example","dir":"","previous_headings":"Usage > genecovr script quick start","what":"Example","title":"Gene body coverage analysis to evaluate genome assemblies","text":"example files located PACKAGE_DIR/inst/extdata consisting two psl alignment files containing gmap alignments fasta indices transcript sequences two different assembly versions: nonpolished.fai - fasta index raw assembly polished.fai - fasta index polished assembly transcripts.fai - fasta index transcript sequences transcripts2nonpolished.psl - gmap alignments, transcripts raw assembly transcripts2polished.psl - gmap alignments, transcripts polished assembly Using files labels non pol different assemblies, genecovr input file (called e.g., assemblies.csv) look follows: command run :","code":"nonpol,transcripts2nonpolished.psl,nonpolished.fai,transcripts.fai pol,transcripts2polished.psl,polished.fai,transcripts.fai genecovr assemblies.csv"},{"path":"https://nbisweden.github.io/genecovr/index.html","id":"genecovr-options","dir":"","previous_headings":"Usage > genecovr script quick start","what":"genecovr options","title":"Gene body coverage analysis to evaluate genome assemblies","text":"list genecovr script options, type ’genecovr -h`:","code":"usage: genecovr [-h] [-v] [-p number] [-d OUTPUT_DIRECTORY] [--height HEIGHT] [--width WIDTH] csvfile positional arguments: csvfile csv-delimited file with columns 1. data label 2. mapping file (supported formats: psl) 3. assembly file (fasta or fasta index) 4. transcript file (fasta or fasta index) optional arguments: -h, --help show this help message and exit -v, --verbose print extra output -p number, --cpus number number of cpus [default 1] -d OUTPUT_DIRECTORY, --output-directory OUTPUT_DIRECTORY output directory --height HEIGHT figure height in inches [default 6.0] --width WIDTH figure width in inches [default 6.0]"},{"path":"https://nbisweden.github.io/genecovr/index.html","id":"r-package-vignette","dir":"","previous_headings":"Usage","what":"R package vignette","title":"Gene body coverage analysis to evaluate genome assemblies","text":"Alternatively, import library R script use package functions. See Get started run vignette(\"genecovr\") minimum working example.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairs-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Representation of an alignment pair — AlignmentPairs-class","title":"Representation of an alignment pair — AlignmentPairs-class","text":"Pairs subclass Constructor AlignmentPairs","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairs-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Representation of an alignment pair — AlignmentPairs-class","text":"","code":"AlignmentPairs(query, subject, ...) # S4 method for GRanges,GRanges AlignmentPairs(query, subject, ...)"},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairs-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Representation of an alignment pair — AlignmentPairs-class","text":"query vectorized object representing query subject vectorized object representing subject ... Arguments pass constructor","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairs-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Representation of an alignment pair — AlignmentPairs-class","text":"AlignmentPairs object","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairs-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Representation of an alignment pair — AlignmentPairs-class","text":"AlignmentPairs class extends Pairs-class","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairs-class.html","id":"constructor","dir":"Reference","previous_headings":"","what":"Constructor","title":"Representation of an alignment pair — AlignmentPairs-class","text":"AlignmentPairs(query, subject, ...): Constructs AlignmentPairs object aligning vectors query subject.","code":""},{"path":[]},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairsList-class.html","id":null,"dir":"Reference","previous_headings":"","what":"List of AlignmentPairs instances — AlignmentPairsList-class","title":"List of AlignmentPairs instances — AlignmentPairsList-class","text":"Subclass S4Vectors SimpleList, entry AlignmentPairs object","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairsList-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List of AlignmentPairs instances — AlignmentPairsList-class","text":"","code":"AlignmentPairsList(obj, ...) # S4 method for list AlignmentPairsList(obj)"},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairsList-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List of AlignmentPairs instances — AlignmentPairsList-class","text":"obj list ... ellipsis","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairsList-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List of AlignmentPairs instances — AlignmentPairsList-class","text":"AlignmentPairsList object","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/AlignmentPairsList-class.html","id":"constructor","dir":"Reference","previous_headings":"","what":"Constructor","title":"List of AlignmentPairs instances — AlignmentPairsList-class","text":"AlignmentPairsList(obj, ...): Constructs AlignmentPairsList object input","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/as.data.frame-AlignmentPairsList-method.html","id":null,"dir":"Reference","previous_headings":"","what":"as.data.frame — as.data.frame,AlignmentPairsList-method","title":"as.data.frame — as.data.frame,AlignmentPairsList-method","text":"Convert AlignmentPairsList data.frame.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/as.data.frame-AlignmentPairsList-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"as.data.frame — as.data.frame,AlignmentPairsList-method","text":"","code":"# S4 method for AlignmentPairsList as.data.frame(x, ..., .id = \"id\")"},{"path":"https://nbisweden.github.io/genecovr/reference/as.data.frame-AlignmentPairsList-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"as.data.frame — as.data.frame,AlignmentPairsList-method","text":"x AlignmentPairsList object ... additional parameters lapply .id name id column added dplyr::bind_rows","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/as.data.frame-AlignmentPairsList-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"as.data.frame — as.data.frame,AlignmentPairsList-method","text":"data.frame","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/autoplot.AlignmentPairsList.html","id":null,"dir":"Reference","previous_headings":"","what":"autoplot.AlignmentPairsList — autoplot.AlignmentPairsList","title":"autoplot.AlignmentPairsList — autoplot.AlignmentPairsList","text":"autoplot.AlignmentPairsList","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/autoplot.AlignmentPairsList.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"autoplot.AlignmentPairsList — autoplot.AlignmentPairsList","text":"","code":"# S3 method for AlignmentPairsList autoplot(object, aes, vars, ..., which = \"point\")"},{"path":"https://nbisweden.github.io/genecovr/reference/autoplot.AlignmentPairsList.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"autoplot.AlignmentPairsList — autoplot.AlignmentPairsList","text":"object AlignmentPairsList aes aes mapping vars variable mapping facet plots ... additional parameters ggplot function plot make. 'grid' option makes scatter plot marginal densities","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/breadthOfCoverage.html","id":null,"dir":"Reference","previous_headings":"","what":"breadthOfCoverage — breadthOfCoverage","title":"breadthOfCoverage — breadthOfCoverage","text":"Calculate breadth coverage sequence id","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/breadthOfCoverage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"breadthOfCoverage — breadthOfCoverage","text":"","code":"breadthOfCoverage(x)"},{"path":"https://nbisweden.github.io/genecovr/reference/breadthOfCoverage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"breadthOfCoverage — breadthOfCoverage","text":"x GRangesList object","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/breadthOfCoverage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"breadthOfCoverage — breadthOfCoverage","text":"integer representing sum range widths","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/countSubjectsByCoverage.html","id":null,"dir":"Reference","previous_headings":"","what":"countSubjectsByCoverage — countSubjectsByCoverage","title":"countSubjectsByCoverage — countSubjectsByCoverage","text":"countSubjectsByCoverage","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/countSubjectsByCoverage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"countSubjectsByCoverage — countSubjectsByCoverage","text":"","code":"countSubjectsByCoverage( x, min.coverage = seq(0.25, 1, 0.25), min.match = 0.9, nmax = 5 )"},{"path":"https://nbisweden.github.io/genecovr/reference/countSubjectsByCoverage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"countSubjectsByCoverage — countSubjectsByCoverage","text":"x AlignmentPairs DataFrame object min.coverage coverage cutoffs apply transcripts min.match filter hits fraction matching bases less min.match nmax maximum number subjects count","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/deletions-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Get deletions from an alignment. — deletions","title":"Get deletions from an alignment. — deletions","text":"Get deletions alignment.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/deletions-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get deletions from an alignment. — deletions","text":"","code":"deletions(x, ...)"},{"path":"https://nbisweden.github.io/genecovr/reference/deletions-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get deletions from an alignment. — deletions","text":"x Object representation sequence alignment ... Additional argument list","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/deletions-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get deletions from an alignment. — deletions","text":"numeric","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/divergence-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Get divergence from an alignment — divergence","title":"Get divergence from an alignment — divergence","text":"Get divergence alignment.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/divergence-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get divergence from an alignment — divergence","text":"","code":"divergence(x, ...)"},{"path":"https://nbisweden.github.io/genecovr/reference/divergence-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get divergence from an alignment — divergence","text":"x Object representation sequence alignment ... Additional argument list","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/divergence-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get divergence from an alignment — divergence","text":"numeric","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/geneBodyCoverage.html","id":null,"dir":"Reference","previous_headings":"","what":"Get gene body coverage — geneBodyCoverage","title":"Get gene body coverage — geneBodyCoverage","text":"geneBodyCoverage(obj, ...): calculate gene body coverage input Calculate geneBodyCoverage query sequences","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/geneBodyCoverage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get gene body coverage — geneBodyCoverage","text":"","code":"geneBodyCoverage(obj, ...) # S4 method for AlignmentPairs geneBodyCoverage(obj, min.match = 0.9) # S4 method for AlignmentPairsList geneBodyCoverage(obj, min.match = 0.9, bpparam = NULL)"},{"path":"https://nbisweden.github.io/genecovr/reference/geneBodyCoverage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get gene body coverage — geneBodyCoverage","text":"obj AlignmentPairs object ... additional parameters min.match filter hits fraction matching bases less min.match bpparam BiocParallel parameter object","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/geneBodyCoverage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get gene body coverage — geneBodyCoverage","text":"reduced filtered DataFrame object row transcript. See @details information seqnames seqlengths columns collected corresponding seqinfo object. breadthOfCoverage total width reduced regions transcript corresponds much transcript covered. Dividing breadthOfCoverage total transcript length gives coverage fraction. depthOfCoverage sums ranges estimate many times range present. Dividing depthOfCoverage breadthOfCoverage indicates multiplicity query. queries map multiple subjects, value close 1 indicates query split several subjects, whereas higher value indicates sequence duplication subject level.","code":"The revmap column maps the output ranges to the input ranges as lists of numerical ids. These ids can be used to retrieve the corresponding AlignmentPairs ranges providing a link to the subjects. The hitCoverage lists the width of each reduced hit, and hitStart and hitEnd provide the transcript coordinates of these hits."},{"path":"https://nbisweden.github.io/genecovr/reference/geneBodyCoverage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get gene body coverage — geneBodyCoverage","text":"Given AlignmentPairs object, calculate gene body coverages query sequences. regions. instance, one hit spans coordinates 100-400 another 200-500, merge 100-500. function calculates many overlaps merged, rationale >1 overlaps seqname, sequence associated multiple distinct regions subject sequence. Thus, unit interest query, function seeks identify reduced disjoint regions query sequence map subject.","code":"The function returns a GRanges object with reduced regions, i.e. overlaps are merged. Information about matches and mismatches is currently dropped as it usually is not possible to infer where mismatches occur. Instead, the data column `coverage` simply holds the ratio of the width of the region to the transcript length. Summing up coverages from disjoint regions then gives total coverage of the transcript. The cutoff is used to filter regions based on the ratio of matches to the width of the region. Since the association between query and subject regions is removed, the return value is a GRanges object consisting of the reduced query ranges with a revmap and coverage attribute."},{"path":"https://nbisweden.github.io/genecovr/reference/genecovr-package.html","id":null,"dir":"Reference","previous_headings":"","what":"genecovr: Gene body coverage analysis to evaluate genome assemblies — genecovr-package","title":"genecovr: Gene body coverage analysis to evaluate genome assemblies — genecovr-package","text":"Gene body coverage analysis evaluate genome assemblies.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/genecovr-package.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"genecovr: Gene body coverage analysis to evaluate genome assemblies — genecovr-package","text":"genecovr package provides functionality evaluating gene body coverage metrics genome assemblies. central measurement unit gene transcript model.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/genecovr-package.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"genecovr: Gene body coverage analysis to evaluate genome assemblies — genecovr-package","text":"autoplot: plot GRanges objects gene body coverage metrics","code":""},{"path":[]},{"path":"https://nbisweden.github.io/genecovr/reference/genecovr-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"genecovr: Gene body coverage analysis to evaluate genome assemblies — genecovr-package","text":"Maintainer: Per Unneberg per.unneberg@nbis.se (ORCID)","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/insertions-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Get insertions from an alignment — insertions","title":"Get insertions from an alignment — insertions","text":"Get insertions alignment.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/insertions-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get insertions from an alignment — insertions","text":"","code":"insertions(x, ...) # S4 method for GRanges insertions(x, as.bases = FALSE, ...)"},{"path":"https://nbisweden.github.io/genecovr/reference/insertions-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get insertions from an alignment — insertions","text":"x Object representation sequence alignment ... Additional argument list .bases Get insertions base pairs","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/insertions-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get insertions from an alignment — insertions","text":"numeric","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/matches-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"matches — matches","title":"matches — matches","text":"Get matches alignment. Get mismatches alignment. Get matches parts repeats alignment.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/matches-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"matches — matches","text":"","code":"matches(x, ...) mismatches(x, ...) repmatches(x, ...) # S4 method for AlignmentPairs matches(x) # S4 method for AlignmentPairs mismatches(x) # S4 method for AlignmentPairs repmatches(x)"},{"path":"https://nbisweden.github.io/genecovr/reference/matches-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"matches — matches","text":"x Object representation sequence alignment ... Additional argument list","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/matches-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"matches — matches","text":"numeric numeric numeric","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/plot.AlignmentPairsList.html","id":null,"dir":"Reference","previous_headings":"","what":"plot — plot.AlignmentPairsList","title":"plot — plot.AlignmentPairsList","text":"plot AlignmentPairsList","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/plot.AlignmentPairsList.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"plot — plot.AlignmentPairsList","text":"","code":"# S3 method for AlignmentPairsList plot(x, ...)"},{"path":"https://nbisweden.github.io/genecovr/reference/plot.AlignmentPairsList.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"plot — plot.AlignmentPairsList","text":"x object plot ... additional arguments autoplot","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/psl-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"methods-psl — psl methods","title":"methods-psl — psl methods","text":"Methods dealing psl data","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/psl-methods.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"methods-psl — psl methods","text":"Methods dealing Pattern Space Layout (psl) file format. See http://genome.ucsc.edu/FAQ/FAQformat.html information.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/query-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve query from object — query","title":"Retrieve query from object — query","text":"object query slot retrieve query object. object query slot set query.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/query-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve query from object — query","text":"","code":"query(x, ...) query(x) <- value # S4 method for AlignmentPairs query(x) # S4 method for AlignmentPairs,GRanges query(x) <- value"},{"path":"https://nbisweden.github.io/genecovr/reference/query-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve query from object — query","text":"x object representing alignment ... Additional arguments value object representing query","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/query-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve query from object — query","text":"query object object representing alignment updated query slot","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/readFastaIndex.html","id":null,"dir":"Reference","previous_headings":"","what":"readFastaIndex — readFastaIndex","title":"readFastaIndex — readFastaIndex","text":"Read fasta index file","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/readFastaIndex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"readFastaIndex — readFastaIndex","text":"","code":"readFastaIndex(fai, ...)"},{"path":"https://nbisweden.github.io/genecovr/reference/readFastaIndex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"readFastaIndex — readFastaIndex","text":"fai fasta index file ... additional parameters pass GenomeInfoDb::Seqinfo","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/readFastaIndex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"readFastaIndex — readFastaIndex","text":"Seqinfo object","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/readFastaIndex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"readFastaIndex — readFastaIndex","text":"","code":"fai <- system.file(\"extdata\", \"polished.fai\", package=\"genecovr\") sinfo <- readFastaIndex(fai)"},{"path":"https://nbisweden.github.io/genecovr/reference/readPsl.html","id":null,"dir":"Reference","previous_headings":"","what":"readPsl — readPsl","title":"readPsl — readPsl","text":"Read psl output","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/readPsl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"readPsl — readPsl","text":"","code":"readPsl( filename, seqinfo.query = NULL, seqinfo.sbjct = NULL, metadata = list(), ... )"},{"path":"https://nbisweden.github.io/genecovr/reference/readPsl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"readPsl — readPsl","text":"filename input filename seqinfo.query Seqinfo object query (transcripts) seqinfo.sbjct Seqinfo object subject (reference) metadata metadata AlignmentPairs result ... additional parameters","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/readPsl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"readPsl — readPsl","text":"AlignmentPairs object","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/readPsl.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"readPsl — readPsl","text":"Parse Pattern Space Layout (psl) file; see http://genome.ucsc.edu/FAQ/FAQformat.html information psl file format","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/readPsl.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"readPsl — readPsl","text":"","code":"fn <- system.file(\"extdata\", \"transcripts2polished.psl\", package=\"genecovr\") ap <- readPsl(fn) #> reading file /home/runner/work/_temp/Library/genecovr/extdata/transcripts2polished.psl #> manually inferring seqinfo for query #> manually inferring seqinfo for subject #> Processed 239 lines in 0.078 secs"},{"path":"https://nbisweden.github.io/genecovr/reference/reduceHitCoverage.html","id":null,"dir":"Reference","previous_headings":"","what":"reduceHitCoverage — reduceHitCoverage","title":"reduceHitCoverage — reduceHitCoverage","text":"Reduce hit coverage seqname","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/reduceHitCoverage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"reduceHitCoverage — reduceHitCoverage","text":"","code":"reduceHitCoverage(x, min.match = 0.9)"},{"path":"https://nbisweden.github.io/genecovr/reference/reduceHitCoverage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"reduceHitCoverage — reduceHitCoverage","text":"x AlignmentPairs object min.match filter hits fraction matching bases less min.match","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/reduceHitCoverage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"reduceHitCoverage — reduceHitCoverage","text":"reduced filtered GRanges object","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/reduceHitCoverage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"reduceHitCoverage — reduceHitCoverage","text":"Given AlignmentPairs object, reduce overlapping query regions. instance, one hit spans coordinates 100-400 another 200-500, merge 100-500. function calculates many overlaps merged, rationale >1 overlaps seqname, sequence associated multiple distinct regions subject sequence. Thus, unit interest query, function seeks identify reduced disjoint regions query sequence map subject.","code":"The function returns a GRanges object with reduced regions, i.e. overlaps are merged. Information about matches and mismatches is currently dropped as it usually is not possible to infer where mismatches occur. Instead, the data column `coverage` simply holds the ratio of the width of the region to the transcript length. Summing up coverages from disjoint regions then gives total coverage of the transcript. The cutoff is used to filter regions based on the ratio of matches to the width of the region. Since the association between query and subject regions is removed, the return value is a GRanges object consisting of the reduced query ranges with a revmap and coverage attribute."},{"path":"https://nbisweden.github.io/genecovr/reference/reduceHitCoverage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"reduceHitCoverage — reduceHitCoverage","text":"","code":"ranges <- IRanges::IRanges( start=c(100, 200, 700), end=c(400, 500, 1000) ) qry <- GenomicRanges::GRanges( ranges=ranges, seqnames=c(\"t1\"), seqinfo=GenomeInfoDb::Seqinfo(seqnames=c(\"t1\"), seqlengths=c(1050)) ) ranges <- IRanges::IRanges( start=c(1000, 1000, 1000), end=c(1300, 1300, 1300) ) sbj <- GenomicRanges::GRanges(ranges=ranges, seqnames=c(\"c1\", \"c2\", \"c1\")) x <- AlignmentPairs(query=qry, subject=sbj, matches=c(300, 290, 280)) if (FALSE) gr <- reduceHitCoverage(x, 0.1)"},{"path":"https://nbisweden.github.io/genecovr/reference/sbjct-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve subject from object — sbjct","title":"Retrieve subject from object — sbjct","text":"object subject slot retrieve subject object. object subject slot set subject.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/sbjct-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve subject from object — sbjct","text":"","code":"sbjct(x, ...) sbjct(x) <- value # S4 method for AlignmentPairs sbjct(x) # S4 method for AlignmentPairs,GRanges sbjct(x) <- value"},{"path":"https://nbisweden.github.io/genecovr/reference/sbjct-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve subject from object — sbjct","text":"x object representing alignment ... Additional arguments value object representing subject","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/sbjct-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve subject from object — sbjct","text":"object representing subject object representing alignment updated subject slot","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/score-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve score from object — score","title":"Retrieve score from object — score","text":"object score slot retrieve score object.","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/score-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve score from object — score","text":"","code":"score(x, ...)"},{"path":"https://nbisweden.github.io/genecovr/reference/score-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve score from object — score","text":"x object representing alignment ... Additional arguments","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/score-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve score from object — score","text":"numeric","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/sequence-data-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"methods-sequence-data — sequence data methods","title":"methods-sequence-data — sequence data methods","text":"Methods dealing sequence data","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/summarizeGeneBodyCoverage.html","id":null,"dir":"Reference","previous_headings":"","what":"summarizeGeneBodyCoverage — summarizeGeneBodyCoverage","title":"summarizeGeneBodyCoverage — summarizeGeneBodyCoverage","text":"summarizeGeneBodyCoverage","code":""},{"path":"https://nbisweden.github.io/genecovr/reference/summarizeGeneBodyCoverage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"summarizeGeneBodyCoverage — summarizeGeneBodyCoverage","text":"","code":"summarizeGeneBodyCoverage(x, min.coverage = seq(0, 1, 0.05), min.match = 0.9)"},{"path":"https://nbisweden.github.io/genecovr/reference/summarizeGeneBodyCoverage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"summarizeGeneBodyCoverage — summarizeGeneBodyCoverage","text":"x AlignmentPairs DataFrame object min.coverage coverage cutoffs apply transcripts min.match filter hits fraction matching bases less min.match","code":""}]