Refactoring for Github actions

QuackenbushLab · Nov 12, 2024 · 616b5be · 616b5be
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,8 +2,20 @@ Package: NetworkDataCompanion
 Title: Tools for Analyzing TCGA and GTEx Data
 Version: 0.0.0.9000
 Authors@R: 
-    person("First", "Last", , "[email protected]", role = c("aut", "cre"),
-           comment = c(ORCID = "YOUR-ORCID-ID"))
+    person("Soel", "Micheletti", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0001-5402-9237"))
+    person("Chen", "Chen",
+                        email = "",role = "aut", comment = c(ORCID = "0000-0002-8042-7201")),
+    person("Kate", "Shutta",
+                        email = "",role = "aut", comment = c(ORCID = "0000-0003-0402-3771")),
+    person("Panagiotis", "Mandros", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0009-0008-9638-9722")),
+    person("Viola", "Fanfani", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0003-3852-6908")),
+    person("Jonas", "Fischer", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0000-0000-0000")),
+Author: Soel Micheletti
+Maintainer: Kate Hoff Shutta <[email protected]>
 Description: An R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo (https://netzoo.github.io).
 License: GPL-3
 biocViews:
@@ -16,6 +28,7 @@ Depends:
   GenomicDataCommons,
   huge,
   magrittr,
+  methods,
   org.Hs.eg.db, 
   presto,
   recount,

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,4 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export("CreateNetworkDataCompanionObject")
+export(CreateNetworkDataCompanionObject)
 exportClasses(NetworkDataCompanion)
+import(methods)
diff --git a/R/NetworkDataCompanion.R b/R/NetworkDataCompanion.R
diff --git a/man/NetworkDataCompanion.Rd b/man/NetworkDataCompanion.Rd
@@ -1,5 +1,5 @@
 \name{NetworkDataCompanion}
-\alias{NetworkDataCompanion}
+\alias{\S4method{NetworkDataCompanion}}
 
 \title{A package for easy and reproducible wrangling of TCGA and GTEx data.}
 

diff --git a/man/convertBetaToM.Rd b/man/convertBetaToM.Rd
@@ -1,12 +1,12 @@
 \name{convertBetaToM}
-\alias{convertBetaToM}
+\alias{\S4method{convertBetaToM}{NetworkDataCompanion}}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{Convert methylation beta values to M-values.}
 \description{
 This function uses the typical logit base 2 transformation to convert from methylation beta values (in the [0,1] range) to m-values (on the real line). The formula is m = log2(beta/(1-beta)).
 }
 \usage{
-convertBetaToM(methylation_betas)
+\S4method{convertBetaToM}{NetworkDataCompanion}(methylation_betas)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{

diff --git a/man/estimateCellCountsEpiSCORE.Rd b/man/estimateCellCountsEpiSCORE.Rd
@@ -1,12 +1,12 @@
 \name{estimateCellCountsEpiSCORE}
-\alias{estimateCellCountsEpiSCORE}
+\alias{\S4method{estimateCellCountsEpiSCORE}{NetworkDataCompanion}}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{Run the EpiSCORE algorithm to estimate cell type proportions.}
 \description{
 This function applies the `constAvBetaTSS` and `wRPC` functions from the EpiSCORE R package within the TCGA data structure. The `wRPC` parameters used are the defaults: `useW=TRUE`, `wth=0.4`, and `maxit=100`.
 }
 \usage{
-estimateCellCountsEpiSCORE(methylation_betas, tissue, array = "450k")
+\S4method{estimateCellCountsEpiSCORE}{NetworkDataCompanion}(methylation_betas, tissue, array = "450k")
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{

diff --git a/man/extractSampleAndGeneInfo.Rd b/man/extractSampleAndGeneInfo.Rd
@@ -1,22 +1,19 @@
 \name{extractSampleAndGeneInfo}
-\alias{extractSampleAndGeneInfo}
+\alias{\S4method{extractSampleAndGeneInfo}{NetworkDataCompanion}}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{
 Extracts experiment-specific information and metadata from ranged summarized experiment object.
 }
 \description{
-%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+Extracts experiment-specific information and metadata from ranged summarized experiment object.
 }
 \usage{
-extractSampleAndGeneInfo(expression_rds_obj)
+\S4method{extractSampleAndGeneInfo}{NetworkDataCompanion}(expression_rds_obj)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{
   \item{expression_rds_obj}{A ranged summarized experiment object}
 }
-\details{
-%%  ~~ If necessary, more details than the description above ~~
-}
 \value{
 %%  ~Describe the value returned
 %%  If it is a LIST, use
@@ -26,20 +23,8 @@ extractSampleAndGeneInfo(expression_rds_obj)
 \item{rds_sample_info}{metadata about the samples (columns)}
 \item{rds_gene_info}{metadata about the genes (rows)}
 }
-\references{
-%% ~put references to the literature/web site here ~
-}
 \author{
 Jonas Fischer (jfischer@hsph.harvard.edu)
 }
-\note{
-%%  ~~further notes~~
-}
 
 %% ~Make other sections like Warning with \section{Warning }{....} ~
-
-\seealso{
-%% ~~objects to See Also as \code{\link{help}}, ~~~
-}
-\examples{
-}
diff --git a/man/filterBarcodesIntersection.Rd b/man/filterBarcodesIntersection.Rd
@@ -1,5 +1,5 @@
 \name{filterBarcodesIntersection}
-\alias{filterBarcodesIntersection}
+\alias{\S4method{filterBarcodesIntersection}{NetworkDataCompanion}}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{
 Convenience wrapper function for \code{mapBarcodeToBarcode} that applies the function directly to two data frames.
@@ -8,7 +8,7 @@ Convenience wrapper function for \code{mapBarcodeToBarcode} that applies the fun
 This function returns a list of the two argument data frames, intersected, and the second frame ordered to match the first. NOTE: Ordering is done based on columns, which are expected to be named by TCGA barcodes.
 }
 \usage{
-filterBarcodesIntersection(exp1, exp2)
+\S4method{filterBarcodesIntersection}{NetworkDataCompanion}(exp1, exp2)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{

diff --git a/man/filterChromosome.Rd b/man/filterChromosome.Rd
@@ -1,5 +1,5 @@
 \name{filterChromosome}
-\alias{filterChromosome}
+\alias{\S4method{filterChromosome}{NetworkDataCompanion}}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{
 Filter for genes in a particular chromosome or chromosomes.
@@ -8,7 +8,7 @@ Filter for genes in a particular chromosome or chromosomes.
 This function filters for genes in a particular chromosome or chromosomes.
 }
 \usage{
-filterChromosome(rds_gene_info, chroms)
+\S4method{filterChromosome}{NetworkDataCompanion}(rds_gene_info, chroms)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{

diff --git a/man/filterDuplicatesSeqDepth.Rd b/man/filterDuplicatesSeqDepth.Rd
@@ -1,5 +1,5 @@
 \name{filterDuplicatesSeqDepth}
-\alias{filterDuplicatesSeqDepth}
+\alias{\S4method{filterDuplicatesSeqDepth}{NetworkDataCompanion}}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{
 A function to filter duplicates based on RNA sequencing depth.
@@ -8,7 +8,7 @@ A function to filter duplicates based on RNA sequencing depth.
 This function filters out duplicates based on RNA-seq, keeping the samples with maximum read depth. Returns indices of samples to KEEP.
 }
 \usage{
-filterDuplicatesSeqDepth(expression_count_matrix)
+\S4method{filterDuplicatesSeqDepth}{NetworkDataCompanion}(expression_count_matrix)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{

diff --git a/man/filterDuplicatesSeqDepthOther.Rd b/man/filterDuplicatesSeqDepthOther.Rd
@@ -1,5 +1,5 @@
 \name{filterDuplicatesSeqDepthOther}
-\alias{filterDuplicatesSeqDepthOther}
+\alias{\S4method{filterDuplicatesSeqDepthOther}{NetworkDataCompanion}}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{A version of \code{filterDuplicatesSeqDepth} to handle the case when sequencing depth is not available.
 }
@@ -8,7 +8,7 @@ This function takes a random duplicate if no info is available on sequencing dep
 }
 
 \usage{
-filterDuplicatesSeqDepthOther(expression_count_matrix, tcga_barcodes)
+\S4method{filterDuplicatesSeqDepthOther}{NetworkDataCompanion}(expression_count_matrix, tcga_barcodes)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{

diff --git a/man/filterGenesByTPM.Rd b/man/filterGenesByTPM.Rd
@@ -1,5 +1,5 @@
 \name{filterGenesByTPM}
-\alias{filterGenesByTPM}
+\alias{\S4method{filterGenesByTPM}{NetworkDataCompanion}}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{
 Filter genes based on minimum expression level (TPM) across samples.
@@ -8,7 +8,7 @@ Filter genes based on minimum expression level (TPM) across samples.
 Filter all genes which have at least \code{tpm_threshold} TPM scores in at least \code{sample_fraction} of samples.
 }
 \usage{
-filterGenesByTPM(expression_tpm_matrix, tpm_threshold, sample_fraction)
+\S4method{filterGenesByTPM}{NetworkDataCompanion}(expression_tpm_matrix, tpm_threshold, sample_fraction)
 }
 \arguments{
   \item{expression_tpm_matrix}{A data frame extracted from a \code{RangedSummarizedExperiment} object containing expression data using the \code{extractSampleAndGeneInfo} function.}

diff --git a/man/filterGenesProteins.Rd b/man/filterGenesProteins.Rd
@@ -1,21 +1,17 @@
 \name{filterGenesProteins}
-\alias{filterGenesProteins}
+\alias{\S4method{filterGenesProteins}{NetworkDataCompanion}}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{Filtering protein coding genes through an rds object.
 }
 \description{
 Filtering protein coding genes through an rds object.
 }
 \usage{
-filterGenesProteins(rds_gene_info)
+\S4method{filterGenesProteins}{NetworkDataCompanion}(rds_gene_info)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{
   \item{rds_gene_info}{rds info object of genes, usually extracted from row information from recount retrieved rds expression objects.}
-}
-\details{
-%%  ~~ If necessary, more details than the description above ~~
-
 }
 \value{
  Array of indices that correspond to the protein coding genes in the rds gene info table.
@@ -24,5 +20,3 @@ filterGenesProteins(rds_gene_info)
 \author{
 Jonas Fischer (jfischer@hsph.harvard.edu)
 }
-\references{
-}
diff --git a/man/filterPurity.Rd b/man/filterPurity.Rd
@@ -1,5 +1,5 @@
 \name{filterPurity}
-\alias{filterPurity}
+\alias{\S4method{filterPurity}{NetworkDataCompanion}}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{
 Filter samples based on tumor purity.
@@ -8,7 +8,7 @@ Filter samples based on tumor purity.
 This function filters a character vector of TCGA barcodes for tumor purity based on a particular method and threshold.
 }
 \usage{
-filterPurity(TCGA_barcodes, method="ESTIMATE", threshold=.6)
+\S4method{filterPurity}{NetworkDataCompanion}(TCGA_barcodes, method="ESTIMATE", threshold=.6)
 }
 \arguments{
   \item{TCGA_barcodes}{Character vector of TCGA barcodes that the user wishes to filter based on tumor purity.}

diff --git a/man/filterSampleType.Rd b/man/filterSampleType.Rd
@@ -1,13 +1,13 @@
 \name{filterSampleType}
-\alias{filterSampleType}
+\alias{\S4method{filterSampleType}{NetworkDataCompanion}}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{
   Filter samples based on sample type.
 }
 \description{This function filters samples based on TCGA sample types.
 }
 \usage{
-  filterSampleType(TCGA_barcodes, types_of_samples)
+  \S4method{filterSampleType}{NetworkDataCompanion}(TCGA_barcodes, types_of_samples)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{

diff --git a/man/filterTumorType.Rd b/man/filterTumorType.Rd
@@ -1,13 +1,13 @@
 \name{filterTumorType}
-\alias{filterTumorType}
+\alias{\S4method{filterTumorType}{NetworkDataCompanion}}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{
 Filter samples based on tumor type.
 }
 \description{This function filters samples based on tumor type. Some examples are: "Primary Tumor", "Solid Tissue Normal", "Primary Blood Derived Cancer - Peripheral Blood". This function is particularly useful for excluding normal samples from analyses.
 }
 \usage{
-filterTumorType(TCGA_barcodes, type_of_tumor, rds_info)
+\S4method{filterTumorType}{NetworkDataCompanion}(TCGA_barcodes, type_of_tumor, rds_info)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{

diff --git a/man/geneNameToENSG.Rd b/man/geneNameToENSG.Rd
@@ -1,13 +1,13 @@
 \name{geneNameToENSG}
-\alias{geneNameToENSG}
+\alias{\S4method{geneNameToENSG}{NetworkDataCompanion}}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{
 Convert from gene name to Ensembl stable id.
 }
 \description{Given an input character vector of gene names, this function converts them to Ensembl stable IDs. Note from \url{https://useast.ensembl.org/Help/Faq?id=488}: "An Ensembl stable ID consists of five parts: ENS(species)(object type)(identifier).(version)."}
 
 \usage{
-geneNameToENSG(gene_names, version = FALSE)
+\S4method{geneNameToENSG}{NetworkDataCompanion}(gene_names, version = FALSE)
 }
 \arguments{
   \item{gene_names}{Character vector of gene names.}

diff --git a/man/getGeneInfo.Rd b/man/getGeneInfo.Rd
@@ -1,13 +1,13 @@
 \name{getGeneInfo}
-\alias{getGeneInfo}
+\alias{\S4method{getGeneInfo}{NetworkDataCompanion}}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{
 Retrieve a variety of gene information based on gene name or Ensemble stable ID.
 }
 \description{ This function uses the \code{gene_mapping} attribute of the NetworkDataCompanion object to provide information on \code{seqid}, \code{source},\code{start},\code{end},\code{strand}, \code{gene_id}, \code{gene_name}, \code{gene_type}, and \code{gene_id_no_ver}.
 }
 \usage{
-getGeneInfo(gene_names_or_ids)
+\S4method{getGeneInfo}{NetworkDataCompanion}(gene_names_or_ids)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{

diff --git a/man/logCPMNormalization.Rd b/man/logCPMNormalization.Rd
@@ -1,21 +1,17 @@
 \name{logCPMNormalization}
-\alias{logCPMNormalization}
+\alias{\S4method{logCPMNormalization}{NetworkDataCompanion}}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{Function to compute CPM values from raw counts.
 }
 \description{
 This function computes CPM values from raw expression counts using the edgeR package as a backend.
 }
 \usage{
-logCPMNormalization(exp_count_mat)
+\S4method{logCPMNormalization}{NetworkDataCompanion}(exp_count_mat)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{
   \item{exp_count_mat}{Matrix or data.frame of raw expression counts.}
-}
-\details{
-%%  ~~ If necessary, more details than the description above ~~
-
 }
 \value{
 \item{counts}{The original count matrix passed as argument to this function.}

diff --git a/man/logTPMNormalization.Rd b/man/logTPMNormalization.Rd
@@ -1,5 +1,5 @@
 \name{logTPMNormalization}
-\alias{logTPMNormalization}
+\alias{\S4method{logTPMNormalization}{NetworkDataCompanion}}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{
 Function for within-array normalization of a RangedSummarizedExperiment object with log transcripts per million (TPM) normalization.
@@ -9,7 +9,7 @@ Returns a named list with raw counts (useful for duplicate filtering based on se
 and the actual log TPM. A pseudocount of 1 is added to each TPM value for this function, so returned "log TPM" values actually correspond to log(TPM + 1).
 }
 \usage{
-logTPMNormalization(expression_rds_obj)
+\S4method{logTPMNormalization}{NetworkDataCompanion}(expression_rds_obj)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{

diff --git a/man/mapBarcodeToBarcode.Rd b/man/mapBarcodeToBarcode.Rd
@@ -1,5 +1,5 @@
 \name{mapBarcodeToBarcode}
-\alias{mapBarcodeToBarcode}
+\alias{\S4method{mapBarcodeToBarcode}{NetworkDataCompanion}}
 %- Also NEED an '\alias' for EACH other topic documented here.
 \title{Helper function for mapping two sets of TCGA barcodes to each other.
 }
@@ -13,26 +13,19 @@ There are 4 different pieces of information returned in a named list that are al
 The same information is provided for \code{bc2}.
 }
 \usage{
-mapBarcodeToBarcode(bc1,bc2)
+\S4method{mapBarcodeToBarcode}{NetworkDataCompanion}(bc1,bc2)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{
   \item{bc1}{Character vector of barcodes in the first set.}
   \item{bc2}{Character vector of barcodes in the second set.}
-}
-\details{
-%%  ~~ If necessary, more details than the description above ~~
-
 }
 \value{
 \item{is_inter1}{Boolean vector of the same length as \code{bc1} that indicates which elements of \code{bc1} are present in \code{bc2}.}
 \item{idcs1}{Integer vector of the same length as \code{bc1} that indicates where to find each barcode of \code{bc1} in \code{bc2}, returning \code{NA} if there is no match. That is, \code{idcs1[i] != NA}, then \code{bc1[i] == bc2[idcs1[i]]}}
 \item{is_inter2}{Boolean vector of the same length as \code{bc2} that indicates which elements of \code{bc2} are present in \code{bc1}.}
 \item{idcs2}{Integer vector of the same length as \code{bc2} that indicates where to find each barcode of \code{bc2} in \code{bc1}, returning \code{NA} if there is no match. That is, \code{idcs2[i] != NA}, then \code{bc2[i] == bc1[idcs2[i]]}.}
 }
-\references{
-%% ~put references to the literature/web site here ~
-}
 \author{
 Jonas Fischer (jfischer@hsph.harvard.edu)
 }