View source: R/preprocessing.R
CreateMotifMatrix | R Documentation |
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("-", "-"), ... )
features |
A GRanges object containing a set of genomic features |
pwm |
A |
genome |
Any object compatible with the |
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 |
sep |
A length-2 character vector containing the separators to be used when constructing matrix rownames from the GRanges |
... |
Additional arguments passed to
|
Requires that motifmatchr is installed https://www.bioconductor.org/packages/motifmatchr/.
Returns a sparse matrix
## 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)
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