Import data into a BuxcoDB database

Description

The main purpose of this function is to add data originally retrieved from the retrieveData method into a new or existing BuxcoDB database. This will most frequently be useful in the context of a merging procedure, however it also can facilitate data sharing and/or communication between seperate DBMS systems.

Usage

dbImport(bux.db = NULL, bux.dta, db.name = "merge_test_1.db", debug = FALSE)

Arguments

Details

If only bux.dta is supplied and not bux.db, then a new database will be created and populated at db.name from its contents. If both db.name and bux.dta are supplied then the data.frame will be loaded into the existing database.

Value

A BuxcoDB object pointing to the newly created database.

Author(s)

Daniel Bottomly

See Also

BuxcoDB, retrieveData

Examples

bux.db <- makeBuxcoDB(sample.db.path())

samp.1 <- retrieveData(bux.db, samples="8034x13140_5")
	
test.db <- "test_db.db"
	
if (file.exists(test.db))
{
	file.remove(test.db)
}
	
#create a new database from the output
db.1 <- dbImport(bux.db=NULL, bux.dta=samp.1, db.name=test.db)
	
samples(db.1)
	
test.db.2 <- "test_db_2.db"
	
if (file.exists(test.db.2))
{
	file.remove(test.db.2)
}

samp.2 <- retrieveData(bux.db, samples="8034x13140_11")
	
db.2 <- dbImport(bux.db=db.1, bux.dta=samp.2, db.name=test.db.2)
	
samples(db.2)
	
file.remove(test.db.2)
file.remove(test.db)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(plethy)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/plethy/dbImport.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dbImport
> ### Title: Import data into a BuxcoDB database
> ### Aliases: dbImport
> ### Keywords: utilities
> 
> ### ** Examples
> 
> bux.db <- makeBuxcoDB(sample.db.path())
> 
> samp.1 <- retrieveData(bux.db, samples="8034x13140_5")
> 	
> test.db <- "test_db.db"
> 	
> if (file.exists(test.db))
+ {
+ 	file.remove(test.db)
+ }
> 	
> #create a new database from the output
> db.1 <- dbImport(bux.db=NULL, bux.dta=samp.1, db.name=test.db)
> 	
> samples(db.1)
[1] "8034x13140_5"
> 	
> test.db.2 <- "test_db_2.db"
> 	
> if (file.exists(test.db.2))
+ {
+ 	file.remove(test.db.2)
+ }
> 
> samp.2 <- retrieveData(bux.db, samples="8034x13140_11")
> 	
> db.2 <- dbImport(bux.db=db.1, bux.dta=samp.2, db.name=test.db.2)
> 	
> samples(db.2)
[1] "8034x13140_5"  "8034x13140_11"
> 	
> file.remove(test.db.2)
[1] TRUE
> file.remove(test.db)
[1] TRUE
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>