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.

Usage

RegionStats(object, ...)

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

# S3 method for class 'GRangesAssay'
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

if (FALSE) { # \dontrun{
library(BSgenome.Hsapiens.UCSC.hg38)
RegionStats(
  object = rownames(atac_small),
  genome = BSgenome.Hsapiens.UCSC.hg38
)
} # }
if (FALSE) { # \dontrun{
library(BSgenome.Hsapiens.UCSC.hg38)
RegionStats(
  object = atac_small[["peaks"]],
  genome = BSgenome.Hsapiens.UCSC.hg38
)
} # }
if (FALSE) { # \dontrun{
library(BSgenome.Hsapiens.UCSC.hg38)
RegionStats(
  object = atac_small,
  assay = "bins",
  genome = BSgenome.Hsapiens.UCSC.hg38
)
} # }