derfinder (version 1.6.4)

createBwSample: 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.

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.

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.

See Also

GRanges, export, link{coerceGR}

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