runDEMetaAnalysis: Combine DE analysis results

In RCPA: Consensus Pathway Analysis

Combine DE analysis results

Description

This function performs mata analysis on multiple DE analysis results.

Usage

runDEMetaAnalysis(
  DEResults,
  method = c("stouffer", "fisher", "addCLT", "geoMean", "minP", "REML")
)

Arguments

DEResults	A list of dataframes containing DE analysis results. Each dataframe must have ID, p.value, logFC and logFCSE columns.
method	The method to combine p-values. It can be one of "fisher", "stouffer", "geoMean", "addCLT", "minP", or "REML".

Value

A dataframe containing combined DE analysis results. The dataframe has ID, p.value, pDFR, logFC, and logFCSE columns.

Examples

library(RCPA)
library(SummarizedExperiment)
affyDEExperiment <- loadData("affyDEExperiment")
agilDEExperiment <- loadData("agilDEExperiment")
RNASeqDEExperiment <- loadData("RNASeqDEExperiment")

metaDEResult <- RCPA::runDEMetaAnalysis(list(
    rowData(affyDEExperiment)[1:1000,],
    rowData(agilDEExperiment)[1:1000,],
    rowData(RNASeqDEExperiment)[1:1000,]
), method = "stouffer")

RCPA documentation built on Nov. 21, 2023, 5:08 p.m.