Compute Tn5 insertion bias

Counts the Tn5 insertion frequency for each DNA hexamer.

Usage

InsertionBias(object, ...)

# S3 method for class 'ChromatinAssay5'
InsertionBias(object, genome, region = "chr1:1-249250621", verbose = TRUE, ...)

# S3 method for class 'Seurat'
InsertionBias(
  object,
  genome,
  assay = NULL,
  region = "chr1:1-249250621",
  verbose = TRUE,
  ...
)

Arguments

object

A SeuratObject::Seurat or ChromatinAssay5 object

...

Arguments passed to other methods

genome

A BSgenome::BSgenome object or any other object supported by BSgenome::getSeq. Do showMethods("getSeq") to get the list of all supported object types.

region

Genomic region to use when assessing bias.

verbose

Display messages

assay

Name of assay to use

Value

Returns a Seurat object

Examples

if (FALSE) { # \dontrun{
library(BSgenome.Hsapiens.UCSC.hg38)

region.use <- GenomicRanges::GRanges(
  seqnames = c("chr1", "chr2"),
  IRanges(start = c(1, 1), end = c(195471971, 182113224))
)

InsertionBias(
  object = atac_small,
  genome = BSgenome.Hsapiens.UCSC.hg38,
  region = region.use
)
} # }