How do I split a genomicrange on chromosome and strand?
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1
Entering edit mode
4.4 years ago
endrebak ▴ 930
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 • 1.9k views
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3
Entering edit mode
4.4 years ago
zx8754 11k

Paste the chrom and strand then split as usual:

split(gr, paste(seqnames(gr), strand(gr)))
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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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