context("Test internal functions") library(org.Hs.eg.db) library(reactome.db) data(GSlisttoy) data(CpG2Genetoy) test_that("check prepareAnnot", { colnames(CpG2Gene) = c("Name", "UCSC_RefGene_Name") rownames(CpG2Gene) = CpG2Gene$Name expect_identical(prepareAnnot(CpG2Gene), CpG2Gene) }) test_that("check getGS", { geneids = GS.list[[1]] GOs = suppressMessages( na.omit(unique( select(org.Hs.eg.db, geneids, "GO",keytype = "SYMBOL")$GO))) GOdf = suppressMessages( select(org.Hs.eg.db, GOs, "SYMBOL", keytype = "GO")) genesymbol = GOdf$SYMBOL names(genesymbol) = GOdf$GO GO.list = split(genesymbol, names(genesymbol)) expect_identical(getGS(geneids, "GO"), GO.list) KEGGs = suppressMessages( na.omit(unique( select(org.Hs.eg.db, geneids, "PATH",keytype = "SYMBOL")$PATH))) KEGGdf = suppressMessages( select(org.Hs.eg.db, KEGGs, "SYMBOL", keytype = "PATH")) genesymbol = KEGGdf$SYMBOL names(genesymbol) = KEGGdf$PATH KEGG.list = split(genesymbol, names(genesymbol)) expect_identical(getGS(geneids, "KEGG"), KEGG.list) gene.entrez = suppressMessages( select(org.Hs.eg.db, geneids, columns = "ENTREZID",keytype = "SYMBOL")$ENTREZID) reactome.df = suppressMessages( select(reactome.db, gene.entrez, columns = "REACTOMEID", keytype = "ENTREZID")) reactom2symbol = suppressMessages( select(org.Hs.eg.db, reactome.df$ENTREZID, columns = "SYMBOL", keytype = "ENTREZID")$SYMBOL) names(reactom2symbol) = reactome.df$REACTOMEID reactome.list = split(reactom2symbol, names(reactom2symbol)) expect_identical(getGS(geneids, "Reactome"), reactome.list) })