Signac (version 0.2.4)

RunChromVAR: Run chromVAR

Description

Wrapper to run chromVAR on an assay with a motif object present. Will return a new Seurat assay with the motif activities stored.

Usage

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

Examples

# NOT RUN {
library(BSgenome.Hsapiens.UCSC.hg19)
RunChromVAR(object = atac_small, genome = BSgenome.Hsapiens.UCSC.hg19)
# }