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

In MalteThodberg/CAGEfightR: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

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

if (.Platform$OS.type != "windows") {
# Use the BigWig-files included with the package:
data('exampleDesign')
bw_plus <- system.file('extdata', exampleDesign$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)
}

MalteThodberg/CAGEfightR documentation built on Sept. 11, 2021, 4:42 a.m.