coverageDiff {htSeqTools} | R Documentation |
Computes coverage of sample1 minus coverage of sample2, taking into account that the chromosomes in sample1 and sample2 are not necessarily the same.
coverageDiff(sample1, sample2, chrLength)
sample1 |
Object with reads from sample 1. Typically, a |
sample2 |
Object with reads from sample 2. Typically, a |
chrLength |
Named vector with chromosome lengths. This can be obtained from the Bioconductor annotation packages,
e.g. |
Computation is restricted to chromosomes in names(chrLength)
.
SimpleRleList
with differences in coverage.
sample1 <- RangedData(IRanges(1:10,11:20),space='chr1') sample2 <- RangedData(IRanges(1:10,11:20),space=rep(c('chr1','chr2'),each=5)) chrLength <- c(50,25); names(chrLength) <- c('chr1','chr2') coverageDiff(sample1,sample2,chrLength)