Construct a Motif object containing DNA sequence motif
information and add it to an existing Seurat object or ChromatinAssay.
If running on a Seurat object, AddMotifs will also run
RegionStats to compute the GC content of each peak and store
the results in the feature metadata. PFMs or PWMs are matched to the genome
sequence using the matchMotifs function with
default parameters to construct a matrix of motif positions in genomic
regions.
AddMotifs(object, ...)# S3 method for default
AddMotifs(object, genome, pfm, verbose = TRUE, ...)
# S3 method for ChromatinAssay
AddMotifs(object, genome, pfm, verbose = TRUE, ...)
# S3 method for Assay
AddMotifs(object, genome, pfm, verbose = TRUE, ...)
# S3 method for StdAssay
AddMotifs(object, genome, pfm, verbose = TRUE, ...)
# S3 method for Seurat
AddMotifs(object, genome, pfm, assay = NULL, verbose = TRUE, ...)
When running on a ChromatinAssay or Seurat object,
returns a modified version of the input object. When running on a matrix,
returns a Motif object.
A Seurat object or ChromatinAssay object
Additional arguments passed to other methods
A BSgenome, DNAStringSet, FaFile, or
string stating the genome build recognized by getBSgenome.
A PFMatrixList or PWMatrixList object containing
position weight/frequency matrices to use
Display messages
Name of assay to use. If NULL, use the default assay
motifmatchr