Create motif matrix — CreateMotifMatrix • Signac

Create a motif x feature matrix from a set of genomic ranges, the genome, and a set of position weight matrices.

CreateMotifMatrix(
  features,
  pwm,
  genome,
  score = FALSE,
  use.counts = FALSE,
  sep = c("-", "-"),
  ...
)

Arguments

features: A GRanges object containing a set of genomic features
pwm: A PFMatrixList or PWMatrixList object containing position weight/frequency matrices to use
genome: Any object compatible with the genome argument in matchMotifs
score: Record the motif match score, rather than presence/absence (default FALSE)
use.counts: Record motif counts per region. If FALSE (default), record presence/absence of motif. Only applicable if score=FALSE.
sep: A length-2 character vector containing the separators to be used when constructing matrix rownames from the GRanges
...: Additional arguments passed to matchMotifs

Value

Returns a sparse matrix

Details

Requires that motifmatchr is installed https://www.bioconductor.org/packages/motifmatchr/.

Examples

if (FALSE) {
library(JASPAR2018)
library(TFBSTools)
library(BSgenome.Hsapiens.UCSC.hg19)

pwm <- getMatrixSet(
  x = JASPAR2018,
  opts = list(species = 9606, all_versions = FALSE)
)
motif.matrix <- CreateMotifMatrix(
  features = granges(atac_small),
  pwm = pwm,
  genome = BSgenome.Hsapiens.UCSC.hg19
)
}