filterCounts: filter count data

In EMBL-Hentze-group/DEWSeq: Differential Expressed Windows Based on Negative Binomial Distribution

filter count data

Description

In addition to count data matrix, htseq-clip also creates a max count matrix.
For each window, this file contains the maximum crosslink site count (height) calculated
per nucleotide. This function uses this file to filter the count data file instead of the
default prefiltering on rowSums. Windows failing the threshold
rowSums(maxWindowCount>=countThresh)>=nSamples will be removed from the object.

Usage

filterCounts(object, maxCountFile, countThresh, nsamples)

Arguments

object	DESeqDataSet, see DESeqDataSetFromSlidingWindows
maxCountFile	character file name/path to max count matrix
countThresh	numeric max count threshold
nsamples	numeric number of samples where the max count value must be >= countThresh

Value

DESeq object

EMBL-Hentze-group/DEWSeq documentation built on Oct. 17, 2023, 10:41 p.m.