Description Usage Arguments Value Author(s) References Examples
View source: R/getSQLiteFile.R
This function is the standard method for downloading and unzipping the most recent GEOmetadb SQLite file from the server.
1 | getSQLiteFile(destdir = getwd(), destfile = "GEOmetadb.sqlite.gz")
|
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 |
Prints some diagnostic information to the screen.
Returns the local filename for use later.
Sean Davis <[email protected]>
http://meltzerlab.nci.nih.gov/apps/geo, http://gbnci.abcc.ncifcrf.gov/geo/
1 | ## Not run: geometadbfile <- getSQLiteFile()
|
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
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