[Bioc-sig-seq] GRanges tabulate the coverage

[Dario Strbenac]

Hello,

I'm encountering a problem where I can tabulate coverage results when I've got a GRanges object without seqlengths in it, but when I put seqlengths in it, it gives an error about negative length vectors. Here is my small example.

library(GenomicRanges)
library(BSgenome.Hsapiens.UCSC.hg18)

chrs = paste("chr", c(1:22, "X", "Y"), sep = "")
myGR <- GRanges(seqnames = c("chr1", "chr3", "chr3", "chr3"), ranges = IRanges(100, width = 200), strand = '+')
coverage <- colSums(table(coverage(resize(myGR, 300))))

seqlengths(myGR) <- seqlengths(Hsapiens)[chrs]
coverage <- colSums(table(coverage(resize(myGR, 300))))

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Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia