RunChromVAR function

Run chromVAR

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, ...)

## S3 method for class 'ChromatinAssay'
RunChromVAR(object, genome, motif.matrix = NULL, verbose = TRUE, ...)

## S3 method for class 'Seurat'
RunChromVAR(
  object,
  genome,
  motif.matrix = NULL,
  assay = NULL,
  new.assay.name = "chromvar",
  ...
)

Arguments

• object: A Seurat object
• ...: Additional arguments passed to getBackgroundPeaks
• genome: A BSgenome object or string stating the genome build recognized by getBSgenome.
• motif.matrix: A peak x motif matrix. If NULL, pull the peak x motif matrix from a Motif object stored in the assay.
• verbose: Display messages
• assay: Name of assay to use
• new.assay.name: Name of new assay used to store the chromVAR results. Default is "chromvar".

Returns

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

## Not run:

library(BSgenome.Hsapiens.UCSC.hg19)
RunChromVAR(object = atac_small[["peaks"]], genome = BSgenome.Hsapiens.UCSC.hg19)
## End(Not run)

## Not run:

library(BSgenome.Hsapiens.UCSC.hg19)
RunChromVAR(object = atac_small, genome = BSgenome.Hsapiens.UCSC.hg19)
## End(Not run)