Compute Tn5 insertion bias

Counts the Tn5 insertion frequency for each DNA hexamer.

InsertionBias(object, ...)

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

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

Arguments

object

A Seurat or ChromatinAssay object

...

Additional arguments passed to StringToGRanges

genome

A BSgenome object or any other object supported by 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) {
library(BSgenome.Mmusculus.UCSC.mm10)

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

InsertionBias(
 object = atac_small,
 genome = BSgenome.Mmusculus.UCSC.mm10,
 region = region.use
)
}