RegionStats: Compute base composition information for genomic ranges

Description Usage Arguments Value Examples

View source: R/generics.R

Description

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

Usage

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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

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## 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 documentation built on Dec. 11, 2021, 9:55 a.m.