Compute Tn5 insertion bias
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, ... )
object |
A Seurat or ChromatinAssay object |
... |
Additional arguments passed to |
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 |
Returns a Seurat object
## 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
)
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