addGCBias {chromVAR} | R Documentation

## addGCBias

### Description

Computes GC content for peaks

### Usage

    addGCBias(object, ...)

    ## S4 method for signature 'RangedSummarizedExperiment'
    addGCBias(object,
      genome = GenomeInfoDb::genome(object))

    ## S4 method for signature 'SummarizedExperiment'
    addGCBias(object, peaks,
      genome = GenomeInfoDb::genome(peaks))

### Arguments

`object` | (Ranged)SummarizedExperiment
`...` | additional arguments
`genome` | BSgenome object, by defualt hg19
`peaks` | GenomicRanges with peaks, needed if object is SummarizedExperiment and not RangedSummarizedExperiment

### Value

(Ranged)SummarizedExperiment object with new column in row metadata with the gc content of the peak in question

### Methods (by class)

- `RangedSummarizedExperiment`: method for RangedSummarizedExperiment

- `SummarizedExperiment`: method for SummarizedExperiment

### Examples

    data(example_counts, package = "chromVAR")
    # show example on small part of data
    subset_counts <- example_counts[1:500,]
    library(BSgenome.Hsapiens.UCSC.hg19)
    example_counts <- addGCBias(subset_counts,
                                  genome = BSgenome.Hsapiens.UCSC.hg19)

[Package chromVAR version 1.12.0 Index]