geoConvert: Cross-reference between GEO data types

Description Usage Arguments Value Author(s) References Examples

View source: R/geoConvert.R

Description

A common task is to find all the GEO entities of one type associated with another GEO entity (eg., find all GEO samples associated with GEO platform 'GPL96'). This function provides a very fast mapping between entity types to facilitate queries of this type.

Usage

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geoConvert(in_list, out_type = c("gse", "gpl", "gsm", "gds", "smatrix"), sqlite_db_name = "GEOmetadb.sqlite")

Arguments

in_list

Character vector of GEO entities to convert from.

out_type

Character vector of GEO entity types to which to convert.

sqlite_db_name

The filename of the GEOmetadb sqlite database file

Value

A list of data.frames.

Author(s)

Jack Zhu <[email protected]>

References

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

Examples

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if(file.exists("GEOmetadb.sqlite")) {
  geoConvert('GPL96',out_type='GSM')
} else {
  print("Run getSQLiteFile() to get a copy of the GEOmetadb SQLite file
and then rerun the example")
}

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] "Run getSQLiteFile() to get a copy of the GEOmetadb SQLite file\nand then rerun the example"

GEOmetadb documentation built on Nov. 1, 2018, 2:07 a.m.