Both fragment ends are kept and shifted to the Tn5 cut position.
Duplicated positions are collapsed into a per base count, held in the
score column so that the object can be used like a methylTFR
methylome.
Usage
getTn5Insertions(
dsa,
sampleId,
regions = NULL,
shift = c(4L, -5L),
normalize = TRUE
)
Arguments
- dsa
A DsATAC object.
- sampleId
Sample identifier.
- regions
Optional GRanges restricting the insertions.
- shift
Offsets applied to the forward and reverse fragment ends.
- normalize
If TRUE, counts are scaled to insertions per million.
Value
A GRanges of single base insertion sites.
Examples
if (FALSE) { # \dontrun{
ins <- getTn5Insertions(dsa, "sample_1", regions = peaks)
} # }