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fixes bug where genomeStyle was undefined

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jurhoades committed Aug 1, 2018
1 parent 56ce289 commit 108b0bb5d2c52da9f6b87bb06292cb3703da061f
Showing with 3 additions and 2 deletions.
  1. +3 −2 R/utils.R
@@ -104,7 +104,8 @@ loadReadCountsFromWig <- function(counts, chrs = c(1:22, "X", "Y"), gc = NULL, m
}
## get gender ##
gender <- getGender(counts.raw, counts, gc, map, fracReadsInChrYForMale = fracReadsInChrYForMale, useChrY = useChrY,
centromere=centromere, flankLength=flankLength, targetedSequences = targetedSequences)
centromere=centromere, flankLength=flankLength, targetedSequences = targetedSequences,
genomeStyle = genomeStyle)
}
return(list(counts = counts, gender = gender))
}
@@ -139,7 +140,7 @@ selectFemaleChrXSolution <- function(){
### FUNCTION TO DETERMINE GENDER #################
##################################################
getGender <- function(rawReads, normReads, gc, map, fracReadsInChrYForMale = 0.002, useChrY = TRUE,
centromere=NULL, flankLength=1e5, targetedSequences=NULL){
centromere=NULL, flankLength=1e5, targetedSequences=NULL, genomeStyle="NCBI"){
chrXStr <- grep("X", unique(normReads$space), value = TRUE)
chrYStr <- grep("Y", unique(rawReads$space), value = TRUE)
chrXInd <- normReads$space == chrXStr

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