RCPA (version 0.2.6)

getCommonPathways: 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)

Value

A data frame contains pathway ID and pathway names.

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.

Examples

# \donttest{

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(head(commonPathways))

# }