getSQLiteFile: Download and unzip the most recent GEOmetadb SQLite file

Description Usage Arguments Value Author(s) References Examples

View source: R/getSQLiteFile.R

Description

This function is the standard method for downloading and unzipping the most recent GEOmetadb SQLite file from the server.

Usage

1
getSQLiteFile(destdir = getwd(), destfile = "GEOmetadb.sqlite.gz")

Arguments

destdir

The destination directory of the downloaded file

destfile

The filename of the downloaded file. This filename should end in ".gz" as the unzipping assumes that is the case

Value

Prints some diagnostic information to the screen.

Returns the local filename for use later.

Author(s)

Sean Davis <[email protected]>

References

http://meltzerlab.nci.nih.gov/apps/geo, http://gbnci.abcc.ncifcrf.gov/geo/

Examples

1
## Not run: geometadbfile <- getSQLiteFile()

Example output

Loading required package: GEOquery
Loading required package: Biobase
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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: RSQLite

GEOmetadb documentation built on May 31, 2017, 11 a.m.