CreateMotifMatrix: Create motif matrix

Description Usage Arguments Details Value Examples

View source: R/preprocessing.R

Description

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

Usage

1
2
3
4
5
6
7
8
9
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

Details

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

Value

Returns a sparse matrix

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
## Not run: 
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
)

## End(Not run)

timoast/signac documentation built on Dec. 14, 2021, 11:34 p.m.