runMultiEnrichment: Main understand module function

In Fjeanneret/multiSight: Multi-omics Classification, Functional Enrichment and Network Inference analysis

Main understand module function

Description

Launches functional enrichment of features provided for every databases furnished. Run by utils function runMultiOmicEnrichment

Usage

runMultiEnrichment(
  omicSignature,
  databasesChosen,
  organismDb,
  pvAdjust = "BH",
  minGSSize = 5,
  maxGSSize = 800,
  pvStouffer = 0.1
)

Arguments

omicSignature	Feature lists from each omic data block.
databasesChosen	Which biological database c(reactome, kegg, wikiPathways, MF, CC, BP)
organismDb	Organism provided by user in Home tab.
pvAdjust	pv adjust method (e.g "BH" for Benjamini-Hochberg)
minGSSize, maxGSSize, pvStouffer	Numeric values chosen by user in ui.

Value

Wraps in obj enrichment results for all databases and all omics.

Examples

data("omic2", package = "multiSight")
splitData <- splitDatatoTrainTest(omic2, 0.8)
data.train <- splitData$data.train
data.test <- splitData$data.test

diabloRes <- runSPLSDA(data.train)
diabloModels <- diabloRes$model #sPLS-DA model using all omics.
diabloFeats <- diabloRes$biosignature #selected features for each omic.
id_db <- list(omic1 = "ENSEMBL", omic2 = "ENSEMBL")

if (requireNamespace("org.Mm.eg.db", quietly = TRUE)) 
{
    library(org.Mm.eg.db, warn.conflicts = FALSE) #Organism's database
    featList <- list(Omic1 = c("ENSMUSG00000039621", 
                           "ENSMUSG00000038733", 
                           "ENSMUSG00000062031"), 
                     Omic2 = c("ENSMUSG00000031170", 
                           "ENSMUSG00000077495", 
                           "ENSMUSG00000042992"))
    dbList <- list(Omic1 = "ENSEMBL",
                 Omic2 = "ENSEMBL")
    convFeat <- convertToEntrezid(featList, dbList, "org.Mm.eg.db")

    ## To enrich features
    database <- c("reactome", "MF")
    #runMultiEnrichment_result <- runMultiEnrichment(databasesChosen = database,
    #                                  omicSignature = convFeat,
    #                                  organismDb = "org.Mm.eg.db")
}
  

Fjeanneret/multiSight documentation built on April 6, 2022, 7:59 a.m.