createBw: Export coverage to BigWig files

In lcolladotor/derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

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 createBwSample.

Details

Use at most one core per chromosome.

Value

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

Author(s)

Leonardo Collado-Torres

See Also

GRangesList, export.bw, 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]]


## Exports fullCoverage() output to BigWig files

lcolladotor/derfinder documentation built on Dec. 17, 2024, 4:53 p.m.