convertBED2BigWig: Convert CTSSs stored in different file formats.

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

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)

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