Signac: RegionStats – R documentation

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RegionStats

Compute base composition information for genomic ranges

Description

Compute the GC content, region lengths, and dinucleotide base frequencies for regions in the assay and add to the feature metadata.

Usage

RegionStats(object, ...)

## Default S3 method:
RegionStats(object, genome, verbose = TRUE, ...)

## S3 method for class 'ChromatinAssay'
RegionStats(object, genome, verbose = TRUE, ...)

## S3 method for class 'Seurat'
RegionStats(object, genome, assay = NULL, verbose = TRUE, ...)

Arguments

`object`	A Seurat object, Assay object, or set of genomic ranges
`...`	Arguments passed to other methods
`genome`	A BSgenome object
`verbose`	Display messages
`assay`	Name of assay to use

Value

Returns a dataframe

Examples

## Not run: 
library(BSgenome.Hsapiens.UCSC.hg19)
RegionStats(
  object = rownames(atac_small),
  genome = BSgenome.Hsapiens.UCSC.hg19
)

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

## End(Not run)
## Not run: 
library(BSgenome.Hsapiens.UCSC.hg19)
RegionStats(
  object = atac_small,
  assay = 'bins',
  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