Hello,
I am trying to import a gff file from ucsc genome browser using rtracklayer's "import" function.
Although it imports the file into R without any error, it changes the order of my chromosomes

That is to say it is reordering the chromosomes when it inputs into R
genes = import("file.gff")
names(genes)= "chr1" "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18" "chr19" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" "chr8" "chr9" "chrX" "chrY"

This is giving me some problems when I compute overlaps using countOverlaps ( IntervalTree-class {IRanges}) as my subject has the order  "chr1" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" "chr8" "chr9" "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18" "chr19" "chrX" "chrY"

Any advice would be greatly appreciated.

Thanks!
Kavitha


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