SigFilter: Build a SigFilter

In bedapub/ribiosNGS: Utilities for next-generation sequencing data analysis in ribios

Build a SigFilter

Description

Build a SigFilter

Usage

SigFilter(logFC, posLogFC, negLogFC, pValue, FDR)

EdgeSigFilter(logFC, posLogFC, negLogFC, pValue, FDR, logCPM)

LimmaSigFilter(logFC, posLogFC, negLogFC, pValue, FDR, aveExpr)

Arguments

logFC	Missing or positive numeric
posLogFC	Missing or positive numeric
negLogFC	Missing or negative numeric
pValue	Missing or numeric between 0 and 1
FDR	Missing or numeric between 0 and 1
logCPM	logCPM filter, only valid for EdgeSigFilter
aveExpr	Average expression filter, only valid for LimmaSigFilter

Value

A SigFilter object

Examples

SigFilter()
SigFilter(logFC=2)
SigFilter(negLogFC=-1)
SigFilter(FDR=0.05)

esf <- EdgeSigFilter(logFC=2, FDR=0.05, logCPM=0)
LimmaSigFilter(logFC=1, FDR=0.05, aveExpr=10)

bedapub/ribiosNGS documentation built on Feb. 10, 2025, 12:34 a.m.