Run chromVAR

Source: R/motifs.R

Wrapper to run chromVAR on an assay with a motif object present. Will return a new Seurat assay with the motif activities (the deviations in chromatin accessibility across the set of regions) as a new assay.

RunChromVAR(
  object,
  genome,
  new.assay.name = "chromvar",
  motif.matrix = NULL,
  assay = NULL,
  sep = c(":", "-"),
  verbose = TRUE,
  ...
)

Arguments

object

A Seurat object
genome

A BSgenome object
new.assay.name

Name of new assay used to store the chromVAR results. Default is "chromvar".
motif.matrix

A peak x motif matrix. If NULL, pull the peak x motif matrix from a Motif object stored in the assay.
assay

Name of assay to use
sep

A length-2 character vector containing the separators passed to StringToGRanges.
verbose

Display messages
...

Additional arguments passed to getBackgroundPeaks

Value

Returns a Seurat object with a new assay

Details

See the chromVAR documentation for more information: https://greenleaflab.github.io/chromVAR/index.html

See the chromVAR paper: https://www.nature.com/articles/nmeth.4401

Examples

if (FALSE) {
library(BSgenome.Hsapiens.UCSC.hg19)
RunChromVAR(object = atac_small, genome = BSgenome.Hsapiens.UCSC.hg19)
}