filterLowCovg-DsATAC-method: filterLowCovg-methods

In GreenleafLab/ChrAccR: Analyzing chromatin accessibility data in R

filterLowCovg-methods

Description

Filter regions with low read counts

Usage

## S4 method for signature '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)

Value

a new DsATAC object with low coverage regions removed

Author(s)

Fabian Mueller

GreenleafLab/ChrAccR documentation built on March 22, 2023, 11:42 p.m.