
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",
...
)
Returns a Seurat
object with a new assay
A Seurat object
Additional arguments passed to
getBackgroundPeaks
A BSgenome
object or string stating the genome build
recognized by getBSgenome
.
A peak x motif matrix. If NULL, pull the peak x motif matrix from a Motif object stored in the assay.
Display messages
Name of assay to use
Name of new assay used to store the chromVAR results. Default is "chromvar".
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[["peaks"]], genome = BSgenome.Hsapiens.UCSC.hg19)
}
if (FALSE) {
library(BSgenome.Hsapiens.UCSC.hg19)
RunChromVAR(object = atac_small, genome = BSgenome.Hsapiens.UCSC.hg19)
}
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