sample data doesnt work due to non numeric chromosomes being encoded as NA

piquelab / QuASAR

Quantitative Allele Specific Analysis of Reads. Joint genotyping & ASE inference for RNA-seq data

MIT License

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sample data doesnt work due to non numeric chromosomes being encoded as NA #2

Closed YPHa closed 9 years ago

YPHa commented 9 years ago

due to the line: chrList <- paste("chr", sort(as.numeric(gsub("chr", "", chrList))), sep="") from: scripts/convertPileupToQuasar.R chromosomes such as X get encoded to NA

a worked around this problem by using the naturalsort library: library('naturalsort') chrList <- naturalsort(chrList, decreasing=FALSE, na.last=NA)

ctharve commented 9 years ago

After realizing that reordering the chromosomes was not necessary, we removed those lines from the script. Thank you for pointing this out.