coverageDiff: Compute the difference in coverage between two objects

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

Description

Computes coverage of sample1 minus coverage of sample2, taking into account that the chromosomes in sample1 and sample2 are not necessarily the same.

Usage

coverageDiff(sample1, sample2, chrLength)

Arguments

sample1	Object with reads from sample 1. Typically, a RangedData object.
sample2	Object with reads from sample 2. Typically, a RangedData object.
chrLength	Named vector with chromosome lengths. This can be obtained from the Bioconductor annotation packages, e.g. BSgenome.Dmelanogaster.UCSC.dm3 for drosophila melanogaster, etc.

Details

Computation is restricted to chromosomes in names(chrLength).

Value

SimpleRleList with differences in coverage.

Examples

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)

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