Signac (version 1.13.0)

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

Value

Returns a dataframe

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

Examples

if (FALSE) {
library(BSgenome.Hsapiens.UCSC.hg19)
RegionStats(
  object = rownames(atac_small),
  genome = BSgenome.Hsapiens.UCSC.hg19
)
}
if (FALSE) {
library(BSgenome.Hsapiens.UCSC.hg19)
RegionStats(
  object = atac_small[['peaks']],
  genome = BSgenome.Hsapiens.UCSC.hg19
)
}
if (FALSE) {
library(BSgenome.Hsapiens.UCSC.hg19)
RegionStats(
  object = atac_small,
  assay = 'bins',
  genome = BSgenome.Hsapiens.UCSC.hg19
)
}