Signac: RunChromVAR – R documentation

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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 (the deviations in chromatin accessibility across the set of regions) as a new assay.

Usage

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
`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".

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

Value

Returns a Seurat object with a new assay

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)

Signac

Analysis of Single-Cell Chromatin Data

v1.2.1

MIT + file LICENSE

Authors

Tim Stuart [aut, cre] (<https://orcid.org/0000-0002-3044-0897>), Avi Srivastava [aut] (<https://orcid.org/0000-0001-9798-2079>), Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>), Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>)

Initial release

2021-05-11