Add DNA sequence motif information

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 motifmatchr::matchMotifs() function with default parameters to construct a matrix of motif positions in genomic regions.

Usage

AddMotifs(object, ...)

# Default S3 method
AddMotifs(object, genome, pfm, verbose = TRUE, ...)

# S3 method for class 'GRangesAssay'
AddMotifs(object, genome, pfm, verbose = TRUE, ...)

# S3 method for class 'Assay'
AddMotifs(object, genome, pfm, verbose = TRUE, ...)

# S3 method for class 'StdAssay'
AddMotifs(object, genome, pfm, verbose = TRUE, ...)

# S3 method for class 'Seurat'
AddMotifs(object, genome, pfm, assay = NULL, verbose = TRUE, ...)

Arguments

object

A Seurat object or ChromatinAssay object

...

Additional arguments passed to other methods

genome

A BSgenome, DNAStringSet, FaFile, or string stating the genome build recognized by getBSgenome.

pfm

A PFMatrixList or PWMatrixList object containing position weight/frequency matrices to use

verbose

Display messages

assay

Name of assay to use. If NULL, use the default assay

Value

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.

See also

motifmatchr