AddMotifs: Add DNA sequence motif information

Description Usage Arguments Value

View source: R/generics.R

Description

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.

Usage

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AddMotifs(object, ...)

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

## S3 method for class 'ChromatinAssay'
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.


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