popHUMANDB {AnnotationDbi} | R Documentation |
Creates SQLite file useful for making a SQLite based annotation package. Also produces the schema file which details the schema for the database produced.
popHUMANDB(prefix, chipSrc, metaDataSrc, outputDir, printSchema)
prefix |
prefix is the first part of the eventual desired package name. (ie. "prefix.sqlite") |
chipSrc |
The path and filename to the intermediate database containing the annotation data for the sqlite to build. |
metaDataSrc |
Either a named character vector containing pertinent information
about the metadata OR the path and filename to the intermediate
database containing the metadata information for the package.
If this is a custom package, then it must be a named vector with the following fields: metaDataSrc <- c( DBSCHEMA="the DB schema", ORGANISM="the organism", SPECIES="the species", MANUFACTURER="the manufacturer", CHIPNAME="the chipName", MANUFACTURERURL="the manufacturerUrl") |
outputDir |
Where you would like the output files to be placed. |
printSchema |
Boolean to indicate whether or not to produce an output of the schema (default is FALSE). |
## Not run: ##Set up the metadata my_metaDataSrc <- c( DBSCHEMA="the DB schema", ORGANISM="the organism", SPECIES="the species", MANUFACTURER="the manufacturer", CHIPNAME="the chipName", MANUFACTURERURL="the manufacturerUrl") ##Builds the org.Hs.eg sqlite: popHUMANDB(prefix="org.Hs.eg", chipSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/chipsrc_human.sqlite", metaDataSrc = my_metaDataSrc, printSchema=TRUE) ##Or if the package is a standard package (it probably isn't): ##Builds the org.Hs.eg sqlite: popHUMANDB(prefix="org.Hs.eg", chipSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/chipsrc_human.sqlite", metaDataSrc = "/mnt/cpb_anno/mcarlson/proj/sqliteGen/nli/annosrc/db/metadatasrc.sqlite", printSchema=TRUE) ## End(Not run)