createBwSample {derfinder} | R Documentation

## 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. 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, 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

[Package derfinder version 1.14.0 Index]