bwCommonGenome {CAGEfightR} | R Documentation

## Find a common genome for a series of BigWig files.

### 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

    # 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')

[Package CAGEfightR version 1.2.0 Index]