runPathwayMetaAnalysis: Perform Meta Analysis

In RCPA: Consensus Pathway Analysis

Perform Meta Analysis

Description

This function performs meta analysis on multiple pathway analysis results.

Usage

runPathwayMetaAnalysis(
  PAResults,
  method = c("stouffer", "fisher", "addCLT", "geoMean", "minP", "REML")
)

Arguments

PAResults	A list of at least size two of data frames obtained from pathway analysis
method	A method used to combine pathway analysis results, which can be "stouffer", "fisher", "addCLT", "geoMean", "minP", or "REML"

Details

This function performs meta-analysis on multiple pathway analysis results.

Value

A dataframe of meta analysis results including the following columns:

• ID: The ID of pathway

• name: The name of pathway

• p.value: The meta p-value of pathway

• pFDR: The adjusted meta p-value of pathway using Benjamini-Hochberg method

• score: The combined score of pathway

• normalizedScore: The combined normalized score of pathway

• pathwaySize: The size of pathway

Examples

library(RCPA)
affyFgseaResult <- loadData("affyFgseaResult")
agilFgseaResult <- loadData("agilFgseaResult")
RNASeqFgseaResult <- loadData("RNASeqFgseaResult")

metaPAResult <- RCPA::runPathwayMetaAnalysis(
    list(affyFgseaResult, agilFgseaResult, RNASeqFgseaResult),
    method = "stouffer"
)

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