filterConsensus {cinaR}

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)