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, ... )
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
|
verbose | Display messages |
... | Additional arguments passed to
|
Returns a Seurat
object with a new assay
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
if (FALSE) { library(BSgenome.Hsapiens.UCSC.hg19) RunChromVAR(object = atac_small, genome = BSgenome.Hsapiens.UCSC.hg19) }