Compute Tn5 insertion bias — InsertionBias • Signac

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
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

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
)
}