[BioC] Turning a GRanges Metadata Column into Rle List

[Dario Strbenac]

Anything neater than this available ?

g <- GRanges(c("chr1", "chr2"), IRanges(c(10, 50), c(15, 55)), scores = c(20, 10))
seqlengths(g) <- c(100, 100)
chrRanges <- split(g, seqnames(g))
lapply(chrRanges, function(x)
{
    scoreVect <- rep(NA, seqlengths(x)[1])
    invisible(mapply(function(st, end, score) scoreVect[st:end] <<- score, start(x), end(x), values(x)[,1]))
    Rle(scoreVect)
})

Then, code to define views on these Rle and calculate view summaries.

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Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia