getBiocPlatformMap: Get mappings between GPL and Bioconductor microarry...
In zhujack/GEOmetadb: A compilation of metadata from NCBI GEO

View source: R/getBiocPlatformMap.R

getBiocPlatformMap

R Documentation

Get mappings between GPL and Bioconductor microarry annotation packages

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

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 <zhujack@mail.nih.gov>, Sean Davis <sdavis2@mail.nih.gov>

Examples

## Use the demo GEOmetadb database:
if( !file.exists("GEOmetadb.sqlite") ) {
    demo_sqlfile <- getSQLiteFile(destdir = getwd(), destfile = "GEOmetadb.sqlite.gz", type = "demo")
} else {
    demo_sqlfile <- "GEOmetadb.sqlite"
}

con <- dbConnect(SQLite(), demo_sqlfile)
getBiocPlatformMap(con)[1:5,]
getBiocPlatformMap(con, bioc=c('hgu133a','hgu95av2'))
dbDisconnect(con)
	
## Download the full GEOmetadb database:
## Not run: geometadbfile <- getSQLiteFile()

zhujack/GEOmetadb documentation built on Oct. 26, 2022, 7:32 a.m.