RegionStats function

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, ...)

## 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

Returns

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)