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)

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 1.9.0 Index]