## ----------------------------------------------------------------------------- library('MSEADbi') tmp <- tempdir() ath <- system.file("extdata","MSEA.Ath.pb.db_DATA.csv",package="MSEADbi") meta <- system.file("extdata","MSEA.Ath.pb.db_METADATA.csv",package="MSEADbi") athDf <- read.csv(ath, fileEncoding="utf8") metaDf <- read.csv(meta) # We need to avoid DOT from the column names (to query with the names) names(athDf) <- gsub("\\.", "", names(athDf)) names(metaDf) <- gsub("\\.", "", names(metaDf)) makeMSEAPackage(pkgname = "MSEA.Ath.pb.db", data=athDf, metadata=metaDf, organism = "Arabidopsis thaliana", version = "0.99.0", maintainer = "Kozo Nishida ", author = "Kozo Nishida", destDir = tmp, license = "Artistic-2.0") mseaPackageDir = paste(tmp, "MSEA.Ath.pb.db", sep="/") install.packages(mseaPackageDir, repos=NULL, type="source") ## ----------------------------------------------------------------------------- library(AnnotationDbi) library(MSEA.Ath.pb.db) columns(MSEA.Ath.pb.db) keytypes(MSEA.Ath.pb.db) ids <- c('SMP0012018', 'SMP0012019') select(MSEA.Ath.pb.db, ids, c("MetaboliteID", "CAS", "HMDBID", "ChEBIID", "KEGGID"), "PathBankID") cls <- columns(MSEA.Ath.pb.db) kts <- keytypes(MSEA.Ath.pb.db) kt <- kts[2] ks <- head(keys(MSEA.Ath.pb.db, keytype = kts[2])) res <- select(MSEA.Ath.pb.db, keys = ks, columns = cls, keytype = kt) head(res) ## ----------------------------------------------------------------------------- species(MSEA.Ath.pb.db) dbInfo(MSEA.Ath.pb.db) dbfile(MSEA.Ath.pb.db) dbschema(MSEA.Ath.pb.db) dbconn(MSEA.Ath.pb.db) ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()