addGCBias: addGCBias

In GreenleafLab/chromVAR: Chromatin Variation Across Regions

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)

GreenleafLab/chromVAR documentation built on Aug. 20, 2019, 11:39 a.m.