InsertionBias: Compute Tn5 insertion bias

In timoast/signac: Analysis of Single-Cell Chromatin Data

Compute Tn5 insertion bias

Description

Counts the Tn5 insertion frequency for each DNA hexamer.

Usage

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 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

## 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)

timoast/signac documentation built on Aug. 23, 2024, 1:48 a.m.