Signac (version 1.14.0)

InsertionBias: Compute Tn5 insertion bias

Description

Counts the Tn5 insertion frequency for each DNA hexamer.

Usage

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,
  ...
)

Value

Returns a Seurat object

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

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
)
}