convertToEntrezid: Understand utils function

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

Understand utils function

Description

To convert features to entrezid to enrich.

Usage

convertToEntrezid(featList, fromDbList, organismDb)

Arguments

featList	Feature lists from each omic data block.
fromDbList	Database names vector. One by omic block (e.g. for 2 omics list(omic1 = "SYMBOL", omic2 = "ENSEMBL")). Returned by getDbFromInput() for app.
organismDb	Organism database to convert features.

Value

featConverted

Examples

if (requireNamespace("org.Mm.eg.db", quietly = TRUE))
{
    library(org.Mm.eg.db, warn.conflicts = FALSE)
    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")
    convFeat <- convertToEntrezid(diabloFeats, id_db, "org.Mm.eg.db")


    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")
}

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