getBiocPlatformMap: Get mappings between GPL and Bioconductor microarry...

Description Usage Arguments Value Author(s) References Examples

View source: R/getBiocPlatformMap.R

Description

Query the gpl table and get GPL information of a given list of Bioconductor microarry annotation packages. Note currently the GEOmetadb does not contains all the mappings, but we are trying to construct a relative complete list.

Usage

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getBiocPlatformMap(con, bioc='all')

Arguments

con

Connection to the GEOmetadb.sqlite database

bioc

Character vector of Biocondoctor microarry annotation packages, e.g. c('hgu133plus2','hgu95av2'). 'all' returns all mappings.

Value

A six-column data.frame including GPL title, GPL accession, bioc_package, manufacturer, organism, data_row_count.

Author(s)

Jack Zhu <[email protected]>, Sean Davis <[email protected]>

References

http://meltzerlab.nci.nih.gov/apps/geo

Examples

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if(file.exists('GEOmetadb.sqlite')) {
    con <- dbConnect(SQLite(), "GEOmetadb.sqlite")
	getBiocPlatformMap(con)[1:5,]
	getBiocPlatformMap(con, bioc=c('hgu133a','hgu95av2'))
	dbDisconnect(con)
} else {
  print("You will need to usethe getSQLiteFile() function to get a copy
of the SQLite database file before this example will work")
}

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
[1] "You will need to usethe getSQLiteFile() function to get a copy\nof the SQLite database file before this example will work"

GEOmetadb documentation built on May 2, 2018, 3:52 a.m.