convertBED2BigWig: Convert CTSSs stored in different file formats.

Description Usage Arguments Value Note Examples

View source: R/convert.R

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

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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

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## 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.