extendRanges {htSeqTools} | R Documentation |
This function allows to extend ranges up to a user-specified length, which can be helpful in ChIP-seq analysis.
extendRanges(x, seqLen = 200, chrlength, mc.cores=1)
x |
Object containing reads. |
seqLen |
Desired sequence length after extension. |
chrlength |
Integer vector indicating the length of each
chromosome. |
mc.cores |
Number of cores to use in parallel computations
(passed on to |
A list of IRanges
objects with extended sequence length.
signature(x = "RangedData")
space(x)
indicates the
chromosome, start(x)
and end(x)
the start/end positions of
each read.
signature(x = "list")
Each element in x
is assumed to correspond to a different sample.
David Rossell
set.seed(1) st <- round(rnorm(1000,500,100)) st[st>2000] <- 2000 strand <- rep(c('+','-'),each=500) space <- rep('chr1',length(st)) sample1 <- RangedData(IRanges(st,st+38),strand=strand,space=space) extendRanges(sample1, seqLen=200, chrlength=c(chr1=2000))