motifScores

get motif scores from SummarizedExperiment object

motifScores(object)

# S4 method for SummarizedExperiment
motifScores(object)

Arguments

object
SummarizedExperiment object with scores assay

Value

matrix with scores

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")

motifScores(motif_ix)
#> 3 x 3 sparse Matrix of class "dgCMatrix"
#>      MA0599.1_KLF5 MA0107.1_RELA MA0137.3_STAT1
#> [1,]      7.975145      13.55634        .      
#> [2,]      7.085762       .             16.29401
#> [3,]      7.739609       .             14.81298