Analysing phenotype microarray data: database I/O with PostgreSQL

This is example R code for using opm to store PM data in a PostgreSQL database and retrieving them again.

This code can be used to check whether a database either found in an R or environment variable or identical to the default value (see below) is correctly set up for this purpose. The code also shows how to include a user-defined selection of metadata.

Note: The database must be accessible with localhost as server, the current user as user and without a password, and the tables must have been set up using the SQL that comes with opm.

Author: Markus Goeker

library(opm)
library(RPostgreSQL)

This tries to get the name of the database file from the R or environment variable OPM_POSTGRESQL_DB:

if (exists("OPM_POSTGRESQL_DB")) {
  dbname <- OPM_POSTGRESQL_DB
} else {
  dbname <- Sys.getenv("OPM_POSTGRESQL_DB", "pmdata")
}

print(dbname)

## [1] "pmdata"

conn <- dbConnect("PostgreSQL", dbname = dbname)

Check without metadata

result <- opm_dbcheck(conn)

print(opm_dbnext(2L, conn))

## [1] 1 1 1 1 1 1 1

Check with metadata

if (all(result == "ok")) {

  # addition of metadata columns
  dbGetQuery(conn,
    "ALTER TABLE plates ADD COLUMN strain text, ADD COLUMN replicate integer;")

  # check with metadata
  md <- data.frame(strain = c("X", "Y"), replicate = c(3L, 7L),
    stringsAsFactors = FALSE)
  result2 <- opm_dbcheck(conn, md)

  # removal of metadata columns
  dbGetQuery(conn,
    "ALTER TABLE plates DROP COLUMN strain, DROP COLUMN replicate;")

}

## NULL

Tidying up

dbDisconnect(conn)

## [1] TRUE

rm(conn)

print(result)

##    last1   insert  receive    clear   object  compare    last2 samelast 
##     "ok"     "ok"     "ok"     "ok"     "ok"     "ok"     "ok"     "ok"

stopifnot(result == "ok")
print(result2)

##    last1   insert  receive    clear   object  compare    last2 samelast 
##     "ok"     "ok"     "ok"     "ok"     "ok"     "ok"     "ok"     "ok"

stopifnot(result2 == "ok")


detach("package:RPostgreSQL", unload = TRUE)