extendRanges: Extend reads or sequences by a user-specified number of...

In htSeqTools: Quality Control, Visualization and Processing for High-Throughput Sequencing data

Description

This function allows to extend ranges up to a user-specified length, which can be helpful in ChIP-seq analysis.

Usage

extendRanges(x, seqLen = 200, chrlength, mc.cores=1)

Arguments

x	Object containing reads.
seqLen	Desired sequence length after extension.
chrlength	Integer vector indicating the length of each chromosome. names(chrlength) must match those in x. This argument is used to ensure that no reads are extended beyond the maximum chromosome length.
mc.cores	Number of cores to use in parallel computations (passed on to mclapply).

Value

A list of IRanges objects with extended sequence length.

Methods

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.

Author(s)

David Rossell

Examples

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))

htSeqTools documentation built on May 6, 2019, 3:39 a.m.