AddMotifs: Add DNA sequence motif information

In timoast/signac: Analysis of Single-Cell Chromatin Data

Add DNA sequence motif information

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

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 'Assay'
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 Jan. 1, 2023, 7:39 a.m.