addGCBias {chromVAR} | R Documentation |
Computes GC content for peaks
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))
object |
(Ranged)SummarizedExperiment |
... |
additional arguments |
genome |
BSgenome object, by defualt hg19 |
peaks |
GenomicRanges with peaks, needed if object is SummarizedExperiment and not RangedSummarizedExperiment |
(Ranged)SummarizedExperiment object with new column in row metadata with the gc content of the peak in question
RangedSummarizedExperiment
: method for RangedSummarizedExperiment
SummarizedExperiment
: method for SummarizedExperiment
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)