coverageDiff {htSeqTools} | R Documentation

## Compute the difference in coverage between two objects

### 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)

[Package htSeqTools version 1.30.0 Index]