filterLowCovg-methods — filterLowCovg,DsATAC-method • ChrAccR

Filter regions with low read counts

# S4 method for DsATAC
filterLowCovg(
  .object,
  thresh = 1L,
  reqSamples = 0.75,
  regionTypes = getRegionTypes(.object)
)

Arguments

.object: DsATAC object
thresh: regions with read counts below this threshold will be considered lowly covered regions (default: regions with fewer than 1 read will be discarded)
reqSamples: the percentile of samples required to meet or exceed the threshold in order for a region to be retained. must be in the interval [0, 1) (default: 0.75 = 75 percent)
regionTypes: character vector specifying the names of the region types to which filtering should be applied (default: all region types)

a new DsATAC object with low coverage regions removed

Fabian Mueller