checkCTSSs: Helper for checking files containing CTSSs

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

Description

Checks whether a file (or GRanges/GPos) contains data formatted in the same manner as CAGE Transcription Start Sites (CTSSs): Each basepair of the genome is associated with a single integer count.

Usage

checkCTSSs(object)

## S4 method for signature 'ANY'
checkCTSSs(object)

## S4 method for signature 'GRanges'
checkCTSSs(object)

## S4 method for signature 'character'
checkCTSSs(object)

## S4 method for signature 'GPos'
checkCTSSs(object)

## S4 method for signature 'BigWigFile'
checkCTSSs(object)

Arguments

object

BigWigFile, character, GRanges or GPos: Path to the file storing CTSSs, or an already improted GRanges/GPos.

Value

TRUE if CTSSs are correctly formatted, otherwise a (hopefully) informative error is thrown.

Note

In the case that a character is supplied pointing to a file, checkCTSSs will not check any extensions, but simply try to read it using rtracklayer::import. This means that checkCTSSs can technically analyze BED-files, although CAGEfightR can only import CTSSs from BigWig or bedGraph files.

Examples

if (.Platform$OS.type != "windows") {
# Load example data
data('exampleDesign')
bw_plus <- system.file('extdata',
                       exampleDesign$BigWigPlus,
                       package = 'CAGEfightR')
bw_plus <- BigWigFileList(bw_plus)

# Check raw file
checkCTSSs(bw_plus[[1]])

# Import first, then check
gr  <- import(bw_plus[[1]])
checkCTSSs(gr)
}

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