RCPA (version 0.2.6)

getCommonDEGenes: 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
)

Value

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

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.

Examples

# \donttest{
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(head(commonDEGenes))
# }