bwGenomeCompatibility {CAGEfightR} | R Documentation

## Check if BigWig-files are compatible with a given genome.

### Description

Given a genome, checks whether a series of BigWig-files are compatible by checking if all common seqlevels have equal seqlengths.

### Usage

    bwGenomeCompatibility(plusStrand, minusStrand, genome)

### Arguments

`plusStrand` | BigWigFileList: BigWig files with plus-strand CTSS data.
`minusStrand` | BigWigFileList: BigWig files with minus-strand CTSS data.
`genome` | Seqinfo: Genome information.

### Value

TRUE, raises an error if the supplied genome is incompabtible.

### See Also

Other BigWig functions: `bwCommonGenome`, `bwValid`

### Examples

    # Use the BigWig-files included with the package:
    data('exampleDesign')
    bw_plus <- system.file('extdata', exampleDesign$BigWigPlus,
                           package = 'CAGEfightR')
    bw_minus <- system.file('extdata', exampleDesign$BigWigMinus,
                            package = 'CAGEfightR')

    # Create two named BigWigFileList-objects:
    bw_plus <- BigWigFileList(bw_plus)
    bw_minus <- BigWigFileList(bw_minus)
    names(bw_plus) <- exampleDesign$Name
    names(bw_minus) <- exampleDesign$Name

    # Make a smaller genome:
    si <- seqinfo(bw_plus[[1]])
    si <- si['chr18']

    # Check if it is still compatible:
    bwGenomeCompatibility(plusStrand=bw_plus, minusStrand=bw_minus, genome=si)

[Package CAGEfightR version 1.6.0 Index]