getCommonDEGenes: Get common significant DE genes from multiple DE Analysis...

In RCPA: Consensus Pathway Analysis

Get common significant DE genes from multiple DE Analysis results

Description

Get a list of common significant DE genes from multiple DE Analysis results.

Usage

getCommonDEGenes(
  DEResults,
  pThreshold = 0.05,
  useFDR = TRUE,
  stat = "logFC",
  statThreshold = 0
)

Arguments

DEResults	A list of data frames with the results of DE analysis.
pThreshold	The p-value threshold to determine if a gene is differentially expressed.
useFDR	Use the FDR adjusted p-value instead of the nominal p-value.
stat	The additional statistics column to use for filtering differentially expressed genes.
statThreshold	The absolute value of the statistic threshold to use for filtering differentially expressed genes. Default is 0, which means no filtering.

Value

A data frame wtih three columns: ID (Entrez IDs), Symbol and Description

Examples

library(RCPA)
library(SummarizedExperiment)

affyDEExperiment <- loadData("affyDEExperiment")
agilDEExperiment <- loadData("agilDEExperiment")
RNASeqDEExperiment <- loadData("RNASeqDEExperiment")

DEResults <- list(
    "Affymetrix - GSE5281" = rowData(affyDEExperiment),
    "Agilent - GSE61196"   = rowData(agilDEExperiment),
    "RNASeq - GSE153873"   = rowData(RNASeqDEExperiment)
)

commonDEGenes <- RCPA::getCommonDEGenes(DEResults)

print(commonDEGenes[1:5,1:3])

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