Compute Tn5 insertion bias — InsertionBias • Signac

Counts the Tn5 insertion frequency for each DNA hexamer.

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

if (FALSE) { # \dontrun{
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
)
} # }