diff --git a/NAMESPACE b/NAMESPACE
index 0d35c9c..1d1694d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -26,7 +26,6 @@ export(sv_to_bedpe_file)
export(sv_to_custom_track)
export(tidy_lymphgen)
export(view_mutation_igv)
-import(GAMBLR.data)
import(GAMBLR.helpers)
import(GenomicRanges, except = c("start", "end", "merge", "shift", "union", "intersect", "setdiff", "reduce", "trim"))
import(S4Vectors, except = c("merge", "second", "first", "union", "intersect", "setdiff", "setequal", "rename", "expand", "head", "tail", "end", "start"))
diff --git a/R/build_browser_hub.R b/R/build_browser_hub.R
index 51c7fef..78221e7 100644
--- a/R/build_browser_hub.R
+++ b/R/build_browser_hub.R
@@ -71,7 +71,7 @@
#'
#' @return Nothing.
#'
-#' @import dplyr GAMBLR.helpers
+#' @import dplyr
#' @export
#'
#' @examples
@@ -113,7 +113,8 @@ build_browser_hub = function(maf_data,
contact_email,
visibility = "squish",
bigDataUrl_base = "https://github.com/morinlab/LLMPP/blob/main",
- bedToBigBed_path){
+ bedToBigBed_path,
+ verbose=FALSE){
# check some provided parameter
stopifnot("`these_seq_types` must be one or more of \"genome\" or \"capture\"." =
@@ -134,6 +135,10 @@ build_browser_hub = function(maf_data,
}
)
}else{
+ if(dir.exists(bedToBigBed_path)){
+ #directory was provided, add expected binary name
+ bedToBigBed_path = paste0(bedToBigBed_path,"/bedToBigBed")
+ }
stopifnot("`bedToBigBed_path` points to a non-existent file." =
file.exists(bedToBigBed_path))
}
@@ -147,7 +152,10 @@ build_browser_hub = function(maf_data,
this_seq_type = these_seq_types_i)
}) %>%
suppressMessages
-
+ if(verbose){
+ group_by(these_samples_metadata$genome,seq_type,pathology) %>% tally() %>% print()
+ group_by(these_samples_metadata$capture,seq_type,pathology) %>% tally() %>% print()
+ }
# check provided splitColumnName parameter
stopifnot("`splitColumnName` must be a column name contained in the metadata." =
splitColumnName %in% names(these_samples_metadata[[1]]))
@@ -188,6 +196,9 @@ build_browser_hub = function(maf_data,
regions_bed = dplyr::select(regions_bed, 1,2,3) %>%
arrange( .[[1]], .[[2]] )
temp_bed = tempfile(pattern = "regionsBed_", fileext = ".bed")
+ if(verbose){
+ print(paste("writing temporary file:",temp_bed))
+ }
write.table(regions_bed, temp_bed, quote = FALSE, sep = "\t", row.names = FALSE,
col.names = FALSE)
if(projection == "grch37"){
@@ -213,13 +224,22 @@ build_browser_hub = function(maf_data,
# get maf data from the specified regions and metadata/samples (for each seq type)
if(missing(maf_data)){
maf_data = mapply(function(these_seq_types_i, these_samples_metadata_i){
- get_ssm_by_regions(regions_bed = regions_bed,
+ if(verbose){
+ get_ssm_by_regions(regions_bed = regions_bed,
+ this_seq_type = these_seq_types_i,
+ these_samples_metadata = these_samples_metadata_i,
+ projection = projection,
+ streamlined = FALSE,
+ basic_columns = TRUE)
+ }else{
+ get_ssm_by_regions(regions_bed = regions_bed,
this_seq_type = these_seq_types_i,
these_samples_metadata = these_samples_metadata_i,
projection = projection,
streamlined = FALSE,
basic_columns = TRUE) %>%
- suppressMessages
+ suppressMessages
+ }
}, these_seq_types, these_samples_metadata, SIMPLIFY = FALSE)
}else{
maf_data = mapply(function(these_seq_types_i, these_samples_metadata_i){
diff --git a/R/gene_to_region.R b/R/gene_to_region.R
index 72c06b5..45cb28a 100644
--- a/R/gene_to_region.R
+++ b/R/gene_to_region.R
@@ -29,7 +29,8 @@ gene_to_region = function(gene_symbol,
ensembl_id,
projection = "grch37",
return_as = "region",
- sort_regions = TRUE){
+ sort_regions = TRUE,
+ pad_length = 0){
stopifnot('`projection` parameter must be "grch37" or "hg38"' = projection %in% c("grch37", "hg38"))
stopifnot('`return_as` parameter must be "region", "bed" or "df"' = return_as %in% c("region", "bed", "df"))
@@ -64,7 +65,7 @@ gene_to_region = function(gene_symbol,
region = dplyr::select(gene_coordinates, chromosome, start, end, gene_name, hugo_symbol, ensembl_gene_id) %>%
as.data.frame() %>%
dplyr::filter(chromosome %in% chr_select)
-
+ region = mutate(region, start = start - pad_length, end = end + pad_length)
if(sort_regions){
if(projection == "grch37"){
chrm_num = region$chromosome
diff --git a/R/liftover.R b/R/liftover.R
index 77c3bac..95455bd 100644
--- a/R/liftover.R
+++ b/R/liftover.R
@@ -25,7 +25,7 @@
#' @rawNamespace import(S4Vectors, except = c("merge", "second", "first", "union", "intersect", "setdiff", "setequal", "rename", "expand", "head", "tail", "end", "start"))
#' @rawNamespace import(GenomicRanges, except = c("start", "end", "merge", "shift", "union", "intersect", "setdiff", "reduce", "trim"))
#' @rawNamespace import(rtracklayer, except = c("start", "end"))
-#' @import dplyr tidyr readr GAMBLR.data
+#' @import dplyr tidyr readr
#' @export
#'
#' @examples
diff --git a/man/annotate_sv.Rd b/man/annotate_sv.Rd
index 3c6adc3..7f58b09 100644
--- a/man/annotate_sv.Rd
+++ b/man/annotate_sv.Rd
@@ -10,10 +10,10 @@ annotate_sv(
with_chr_prefix = FALSE,
collapse_redundant = FALSE,
return_as = "bedpe",
- blacklist = c(60565248, 30303126, 187728894, 101357565, 101359747, 161734970,
- 69400840, 65217851, 187728889, 187728888, 187728892, 187728893, 188305164, 72551424,
- 72551425, 72551554, 72551555, 72551558, 72551559, 72551562, 189255425, 189255426,
- 189255461, 189255462),
+ blacklist = c(60565248, 30303126, 187728894, 101357565, 101359747, 161734970, 69400840,
+ 65217851, 187728889, 187728888, 187728892, 187728893, 188305164, 72551424, 72551425,
+ 72551554, 72551555, 72551558, 72551559, 72551562, 189255425, 189255426, 189255461,
+ 189255462),
genome_build = "grch37",
priority_to_be_oncogene = c("MYC", "BCL6")
)
diff --git a/man/build_browser_hub.Rd b/man/build_browser_hub.Rd
index eb72d20..557fa50 100644
--- a/man/build_browser_hub.Rd
+++ b/man/build_browser_hub.Rd
@@ -20,7 +20,8 @@ build_browser_hub(
contact_email,
visibility = "squish",
bigDataUrl_base = "https://github.com/morinlab/LLMPP/blob/main",
- bedToBigBed_path
+ bedToBigBed_path,
+ verbose = FALSE
)
}
\arguments{
diff --git a/man/gene_to_region.Rd b/man/gene_to_region.Rd
index 69600b2..47daf71 100644
--- a/man/gene_to_region.Rd
+++ b/man/gene_to_region.Rd
@@ -9,7 +9,8 @@ gene_to_region(
ensembl_id,
projection = "grch37",
return_as = "region",
- sort_regions = TRUE
+ sort_regions = TRUE,
+ pad_length = 0
)
}
\arguments{
diff --git a/man/make_igv_snapshot.Rd b/man/make_igv_snapshot.Rd
index 9822e9d..d84a059 100644
--- a/man/make_igv_snapshot.Rd
+++ b/man/make_igv_snapshot.Rd
@@ -78,11 +78,15 @@ or the user can directly supply the chromosome, start and end coordinates with t
For more information and examples, refer to the function examples and parameter descriptions.
IMPORTANT: you must be running IGV on the host that is running R and you need to have it listening on a port.
The simplest scenario is to run this command on a terminal (if using a Mac),
-assuming you are using R on gphost10 and you have a ssh config that routes gp10 to that host\preformatted{ssh -X gp10
-}
+assuming you are using R on gphost10 and you have a ssh config that routes gp10 to that host
-then launch IGV (e.e. from a conda installation):\preformatted{conda activate igv; igv &
-}
+\if{html}{\out{}}\preformatted{ssh -X gp10
+}\if{html}{\out{
}}
+
+then launch IGV (e.e. from a conda installation):
+
+\if{html}{\out{}}\preformatted{conda activate igv; igv &
+}\if{html}{\out{
}}
}
\examples{
\dontrun{
diff --git a/man/view_mutation_igv.Rd b/man/view_mutation_igv.Rd
index 5ef7055..e5690d2 100644
--- a/man/view_mutation_igv.Rd
+++ b/man/view_mutation_igv.Rd
@@ -42,11 +42,15 @@ Load bam(s) and view the context around a mutation
Load bam(s) and view the context around a mutation.
IMPORTANT: you must be running IGV on the host that is running R and you need to have it listening on a port.
The simplest scenario is to run this command on a terminal (if using a Mac),
-assuming you are using R on gphost10 and you have a ssh config that routes gp10 to that host\preformatted{ssh -X gp10
-}
+assuming you are using R on gphost10 and you have a ssh config that routes gp10 to that host
-then launch IGV (e.e. from a conda installation):\preformatted{conda activate igv; igv &
-}
+\if{html}{\out{}}\preformatted{ssh -X gp10
+}\if{html}{\out{
}}
+
+then launch IGV (e.e. from a conda installation):
+
+\if{html}{\out{}}\preformatted{conda activate igv; igv &
+}\if{html}{\out{
}}
Then obtain a socket and run this function as per the example.
}