## ----Access1, eval=FALSE------------------------------------------------------ # library("AnnotationHub") ## ----Access2, eval=FALSE------------------------------------------------------ # ah <- AnnotationHub() ## ----Access3, eval=FALSE------------------------------------------------------ # head(mcols(ah)) ## ----Access4, eval=FALSE------------------------------------------------------ # mcols(query(ah, c("MeSHDb", "MeSH.db", "v002"))) ## ----Access5, eval=FALSE------------------------------------------------------ # dbfile1 <- query(ah, c("MeSHDb", "MeSH.db", "v002"))[[1]] # dbfile2 <- query(ah, c("MeSHDb", "MeSH.AOR.db", "v002"))[[1]] # dbfile3 <- query(ah, c("MeSHDb", "MeSH.PCR.db", "v002"))[[1]] # dbfile4 <- query(ah, c("MeSHDb", "Danio rerio", "v002"))[[1]] # dbfile5 <- query(ah, c("MeSHDb", "Pseudomonas aeruginosa PAO1", "v002"))[[1]] ## ----Access6, eval=FALSE------------------------------------------------------ # library("MeSHDbi") # MeSH.db <- MeSHDbi::MeSHDb(dbfile1) # MeSH.AOR.db <- MeSHDbi::MeSHDb(dbfile2) # MeSH.PCR.db <- MeSHDbi::MeSHDb(dbfile3) # MeSH.Dre.eg.db <- MeSHDbi::MeSHDb(dbfile4) # MeSH.Pae.PAO1.eg.db <- MeSHDbi::MeSHDb(dbfile5) ## ----EA1, eval=FALSE---------------------------------------------------------- # library("meshr") # # # dummy geneids for demo # geneid <- keys(MeSH.Pae.PAO1.eg.db, keytype="GENEID") # set.seed(1234) # sig.geneid <- sample(geneid, 500) # # meshParams <- new("MeSHHyperGParams", # geneIds = sig.geneid, # universeGeneIds = geneid, # annotation = "MeSH.Pae.PAO1.eg.db", # meshdb = "MeSH.db", # Newly added parameter from BioC 3.14 # category = "A", # database = "Escherichia coli str. K-12 substr. MG1655", # pvalueCutoff = 0.5, pAdjust = "BH") # meshR <- meshHyperGTest(meshParams) ## ----EA2, eval=FALSE---------------------------------------------------------- # head(summary(meshR)) ## ----EA3, eval=FALSE---------------------------------------------------------- # category(meshParams) <- "B" # database(meshParams) <- "Bacillus subtilis subsp. subtilis str. 168" # meshR <- meshHyperGTest(meshParams) # head(summary(meshR)) ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()