motifCounts

get motif counts from SummarizedExperiment object

motifCounts(object)

# S4 method for 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)
#> 3 x 3 sparse Matrix of class "dgCMatrix"
#>      MA0599.1_KLF5 MA0107.1_RELA MA0137.3_STAT1
#> [1,]             1             1              .
#> [2,]             1             .              1
#> [3,]             1             .              2