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 ChromatinAssay
RunChromVAR(object, genome, motif.matrix = NULL, verbose = TRUE, ...)
# S3 method for Seurat
RunChromVAR(
object,
genome,
motif.matrix = NULL,
assay = NULL,
new.assay.name = "chromvar",
...
)
object | A Seurat object |
---|---|
... | Additional arguments passed to
|
genome | A |
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 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