Compute base composition information for genomic ranges

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

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, ...)

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

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
)
}