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databio / GenomicDistributions

Calculate and plot distributions of genomic ranges
http://code.databio.org/GenomicDistributions
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Assignment operator #174

Closed nsheff closed 2 years ago

nsheff commented 2 years ago

Need to be consistent about assignment operator. This package is using = in general, but some <- has snuck in it.

grep "<-" *
buildReferenceData.R:retrieveFile <- function(source, destDir=NULL){
buildReferenceData.R:getTssFromGTF <- function(source, convertEnsemblUCSC=FALSE, destDir=NULL){
buildReferenceData.R:getGeneModelsFromGTF <- function(source,
buildReferenceData.R:getChromSizesFromFasta <- function(source, destDir=NULL) {
package.R:        "countOverlaps", "distance", "elementMetadata<-", "elementNROWS", 
package.R:        "regionGroupID", "seqlevels<-", "size", "tableCount", "V1", "queryPeak", 
qthist.R:    listOutput <- list("bins"= b,"quantile"= q, "divisions" = div)
utility.R:#' x <- function(var1) {
utility.R:.validateInputs <- function(checkList) {
kkupkova commented 2 years ago

Removed - except in globalVaribles in package.R (probably part of other function from outside GenomicDistributions?)