motifCounts: motifCounts

In motifmatchr: Fast Motif Matching in R

Description

get motif counts from SummarizedExperiment object

Usage

motifCounts(object)

## S4 method for signature 'SummarizedExperiment'
motifCounts(object)

Arguments

object

SummarizedExperiment object with counts assay

Value

matrix with counts

Methods (by class)

• SummarizedExperiment: method for SummarizedExperiment

Examples

data(example_motifs, package = "motifmatchr")

# Make a set of peaks
peaks <- GenomicRanges::GRanges(seqnames = c("chr1","chr2","chr2"),
                ranges = IRanges::IRanges(start = c(76585873,42772928,
                                          100183786),
                                          width = 500))

# Get motif matches for example motifs
motif_ix <- matchMotifs(example_motifs, peaks,
                         genome = "BSgenome.Hsapiens.UCSC.hg19",
                         out = "scores")

motifCounts(motif_ix)

motifmatchr documentation built on Nov. 8, 2020, 8:09 p.m.