## ----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()