filterConsensus: filterConsensus

In cinaR: A Computational Pipeline for Bulk 'ATAC-Seq' Profiles

filterConsensus

Description

Filters lowly expressed peaks from down-stream analyses

Usage

filterConsensus(
  cp,
  filter.method = "custom",
  library.threshold = 2,
  cpm.threshold = 1
)

Arguments

cp	consensus peak matrix, with unique ids at rownames.
filter.method	filtering method for low expressed peaks
library.threshold	number of libraries a peak occurs so that it is not filtered default set to 2
cpm.threshold	count per million threshold for not to filter a peak

Value

returns differentially accessible peaks

Examples

set.seed(123)
cp <- matrix(rexp(200, rate=.1), ncol=20)

## using cpm function from `edgeR` package
cp.filtered <- filterConsensus(cp)

cinaR documentation built on Feb. 4, 2026, 5:13 p.m.