createBwSample: Create a BigWig file with the coverage information for a...

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

Create a BigWig file with the coverage information for a given sample

Description

Given the output of fullCoverage, this function coerces the coverage to a GRanges object using coerceGR and then exports the coverage to a BigWig file using export.bw.

Usage

createBwSample(sample, path = ".", fullCov, keepGR = TRUE, ...)

Arguments

sample	The name or integer index of the sample of interest to coerce to a GRanges object.
path	The path where the BigWig file will be created.
fullCov	A list where each element is the result from loadCoverage used with returnCoverage = TRUE. Can be generated using fullCoverage.
keepGR	If TRUE, the GRanges object created by coerceGR is returned. Otherwise it is discarded.
...	Arguments passed to other methods and/or advanced arguments. Advanced arguments: verbose If TRUE basic status updates will be printed along the way. Passed to coerceGR.

Value

Creates a BigWig file with the coverage information (regions with coverage greater than zero) for a given sample. If keepGR it returns the output from coerceGR.

Author(s)

Leonardo Collado-Torres

See Also

GRanges, export.bw, linkcoerceGR

Examples

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

## Create a BigWig for the first sample in a test directory
dir.create("createBwSample-example")
bw <- createBwSample("ERR009101", "createBwSample-example",
    fullCov = fullCov, seqlengths = c("chr21" = 48129895)
)

## Explore the output
bw

## Exports a single sample to a BigWig file

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