bwCommonGenome: Find a common genome for a series of BigWig files.

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

Description

Finds a common genome for a series of BigWig-files, either using only levels present in all files (intersect) or in any file (union).

Usage

bwCommonGenome(plusStrand, minusStrand, method = "intersect")

Arguments

plusStrand	BigWigFileList: BigWig files with plus-strand CTSS data.
minusStrand	BigWigFileList: BigWig files with minus-strand CTSS data.
method	character: Either 'intersect' or 'union'.

Value

Sorted Seqinfo-object.

See Also

Other BigWig functions: bwGenomeCompatibility(), 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

# Find the smallest common genome (intersect) across the BigWigList-objects:
bwCommonGenome(plusStrand=bw_plus, minusStrand=bw_minus, method='intersect')

# Find the most inclusive genome (union) across the BigWigList-objects:
bwCommonGenome(plusStrand=bw_plus, minusStrand=bw_minus, method='union')
}

CAGEfightR documentation built on Nov. 8, 2020, 5:42 p.m.