View source: R/common-sigPath.R
getCommonPathways | R Documentation |
Query a list of common significant pathways from multiple pathway analysis results.
getCommonPathways(PAResults, pThreshold = 0.05, useFDR = TRUE)
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. |
A data frame contains pathway ID and pathway names.
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))
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