RegionStats: Compute base composition information for genomic ranges

In Signac: Analysis of Single-Cell Chromatin Data

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 or any other object supported by getSeq. Do showMethods("getSeq") to get the list of all supported object types.
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 documentation built on Sept. 11, 2024, 9:30 p.m.