runMultiEnrichment {multiSight} | R Documentation

## 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")
    }

[Package multiSight version 1.2.0 Index]