InsertionBias: Compute Tn5 insertion bias

Description Usage Arguments Value Examples

View source: R/generics.R

Description

Counts the Tn5 insertion frequency for each DNA hexamer.

Usage

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InsertionBias(object, ...)

## S3 method for class 'ChromatinAssay'
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 Seurat or ChromatinAssay object

...

Additional arguments passed to StringToGRanges

genome

A BSgenome object

region

Region to use when assessing bias. Default is human chromosome 1.

verbose

Display messages

assay

Name of assay to use

Value

Returns a Seurat object

Examples

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## Not run: 
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
)

## End(Not run)

Signac documentation built on Dec. 11, 2021, 9:55 a.m.