addGCBias

Computes GC content for peaks

addGCBias(object, ...)

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

# S4 method for 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

# NOT RUN {
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)

# }