derfinder (version 1.6.4)

createBw: Export coverage to BigWig files

Description

Using output from fullCoverage, export the coverage from all the samples to BigWig files using createBwSample.

Usage

createBw(fullCov, path = ".", keepGR = TRUE, ...)

Arguments

fullCov

A list where each element is the result from loadCoverage used with returnCoverage = TRUE. Can be generated using fullCoverage.

path

The path where the BigWig files will be created.

keepGR

If TRUE, the GRanges objects created by coerceGR grouped into a GRangesList are returned. Otherwise they are discarded.

...

Arguments passed to other methods and/or advanced arguments.

Value

• If keepGR = TRUE, then a GRangesList with the output for coerceGR for each of the samples.

Details

Use at most one core per chromosome.

See Also

GRangesList, export, createBwSample, coerceGR

Examples

## Create a small fullCov object with data only for chr21
fullCov <- list('chr21' = genomeDataRaw)

## Keep only 2 samples
fullCov$chr21$coverage <- fullCov$chr21$coverage[c(1, 31)]

## Create the BigWig files for all samples in a test dir
dir.create('createBw-example')
bws <- createBw(fullCov, 'createBw-example')

## Explore the output
bws

## First sample
bws[[1]]

## Note that if a sample has no bases with coverage > 0, the GRanges object
## is empty and no BigWig file is created for that sample.
bws[[2]]