getCommonPathways: Retrieve common significant pathways from multiple pathway...

In RCPA: Consensus Pathway Analysis

Retrieve common significant pathways from multiple pathway analysis results

Description

Query a list of common significant pathways from multiple pathway analysis results.

Usage

getCommonPathways(PAResults, pThreshold = 0.05, useFDR = TRUE)

Arguments

PAResults	A list of data frames with the results of pathway analysis.
pThreshold	The p-value threshold to determine if a pathway is enriched or significant.
useFDR	Use the FDR adjusted p-value instead of the nominal p-value.

Value

A data frame contains pathway ID and pathway names.

Examples

library(RCPA)


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

PAResults <- list(
    "Affymetrix - GSE5281" = affyFgseaResult,
    "Agilent - GSE61196" = agilFgseaResult,
    "RNASeq - GSE153873" = RNASeqFgseaResult
)

commonPathways <- RCPA::getCommonPathways(PAResults)

print(commonPathways[1:6,])

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