createBw: Export coverage to BigWig files

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

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, 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

derfinder documentation built on Dec. 20, 2020, 2 a.m.