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How do I split a genomicrange on chromosome and strand?
library(GenomicRanges)

gr <- GRanges(Rle(c("chr2", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
                   IRanges(1:10, width=10:1, names=head(letters, 10)),
                   Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
                   score=1:10, GC=seq(1, 0, length=10))
split(gr, seqnames(gr))

Gives me a list of chromosomes, but how do I get a list split on chromosome and strand?

genomicranges r bioconductor
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updated by jon.klonowski jon.klonowski • written by endrebak endrebak

1 answer

Paste the chrom and strand then split as usual:

split(gr, paste(seqnames(gr), strand(gr)))
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written by zx8754 zx8754

Wonderful, thanks for the help!

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written by endrebak endrebak

I am trying to split just by chromosome but this does not work for me.

split(gr, seqnames(gr))

Will split everything by chromosome but the object for each chromosome will be the same length, which I assume is the number of sequences in chr1.

Please advise :/

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written by jon.klonowski jon.klonowski

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