convertBED2BigWig {CAGEfightR} | R Documentation

## Convert CTSSs stored in different file formats.

### Description

Collection of functions for converting CTSSs/CTSSs-like data stored in BigWig, bedGraph or BED file formats. BigWig and bedGraph files use a file for each strand, while BED-files stores both strands in a single file. As BigWig files stores info about the chromosome lenghts, conversion from bedGraph/BED to BigWig requires a genome. Note that CAGEfightR will only import BigWig or bedGraph files!

### Usage

    convertBED2BigWig(input, outputPlus, outputMinus, genome)

    convertBED2BedGraph(input, outputPlus, outputMinus)

    convertBedGraph2BigWig(input, output, genome)

    convertBigWig2BedGraph(input, output)

    convertBigWig2BED(inputPlus, inputMinus, output)

    convertBedGraph2BED(inputPlus, inputMinus, output)

### Arguments

`input` | charater: Path to input files holding CTSSs on both strands.
`outputPlus` | character: Path to output files holding CTSSs on plus strand.
`outputMinus` | character: Path to output files holding CTSSs on minus strand.
`genome` | Seqinfo or character: Genome info passed to rtracklayer::import (see note).
`output` | charater: Path to output files holding CTSSs on both strands.
`inputPlus` | character: Path to input files holding CTSSs on plus strand.
`inputMinus` | character: Path to input files holding CTSSs on minus strand.

### Value

TRUE returned invisibly if conversion(s) was succesful, otherwise an error is raised.

### Note

These functions will warn if input files do not have the correct extensions (.bw, .bedGraph, .bed), but otherwise simply pass input to rtracklayer::import. This makes them able to handle compressed files (like .gz). The same applies to the genome argument, which can also be the name of a UCSC genome.

### Examples

    ## Not run:
    # Find paths to BigWig files
    data('exampleDesign')
    bw_plus <- system.file('extdata', exampleDesign$BigWigPlus,
                           package = 'CAGEfightR')
    bw_minus <- system.file('extdata', exampleDesign$BigWigMinus,
                            package = 'CAGEfightR')

    # Designate paths to new files
    n_samples <- length(bw_plus)
    beds <- replicate(n=n_samples, tempfile(fileext=".bed"))
    bg_plus <- replicate(n=n_samples, tempfile(fileext="_plus.bedGraph"))
    bg_minus <- replicate(n=n_samples, tempfile(fileext="_minus.bedGraph"))
    conv_plus <- replicate(n=n_samples, tempfile(fileext="_plus.bw"))
    conv_minus <- replicate(n=n_samples, tempfile(fileext="_minus.bw"))

    # Convert BigWig to BED
    convertBigWig2BED(inputPlus=bw_plus,
                      inputMinus=bw_minus,
                      output=beds)

    # Convert BED to bedGraph
    convertBED2BedGraph(input=beds,
                        outputPlus=bg_plus,
                        outputMinus=bg_minus)

    # Convert BED to bedGraph
    mm9 <- SeqinfoForUCSCGenome("mm9")
    convertBED2BigWig(input=beds,
                      outputPlus=conv_plus,
                      outputMinus=conv_minus,
                      genome=mm9)

    # Check it's still the same data
    x <- import(bw_plus[1])
    y <- import(bg_plus[1])
    z <- import(conv_plus[1])
    all(x == y)
    all(x == z)
    sum(score(x)) ==  sum(score(y))
    sum(score(x)) ==  sum(score(z))

    ## End(Not run)

[Package CAGEfightR version 1.14.0 Index]