Illumina ID Mapping information of all Human expression chips

Description

Welcome to the lumiHumanIDMapping ID mapping Package. The purpose of this package is to provide ID mappings between different types of Illumina identifiers of Human Expression chips and nuIDs, and also mappings from nuIDs to the the most recent Homo sapiens RefSeq release and Entez_Gene_ID. The library includes the data tables corresponding to all released Illumian Human Expression chips before the package releasing date. Each table includes columns "Search_key" ("Search_Key"), "Target" ("ILMN_Gene"), "Accession", "Symbol", "ProbeId" ("Probe_Id") and "nuID". It also includes a nuID_MappingInfo table, which keeps the mapping information of nuID to Accession ID, Entrez_Gene_ID and Symbol. For the version after 1.8.0, all mapping information was based on Illumina manifest files. Information from new versions of manifest files will replace the old ones with the same probe id. The package is supposed to be used together with the Bioconductor lumi package.

You can learn what objects this package supports with the following command:

ls("package:lumiHumanIDMapping")

Each of these objects has their own manual page detailing where relevant data was obtained along with some examples of how to use it.

Examples

  ls("package:lumiHumanIDMapping")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(lumiHumanIDMapping)
Loading required package: lumi
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

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: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lumiHumanIDMapping/lumiHumanIDMapping.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lumiHumanIDMapping
> ### Title: Illumina ID Mapping information of all Human expression chips
> ### Aliases: lumiHumanIDMapping
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   ls("package:lumiHumanIDMapping")
[1] "lumiHumanIDMapping"        "lumiHumanIDMapping_dbInfo"
[3] "lumiHumanIDMapping_dbconn" "lumiHumanIDMapping_dbfile"
[5] "lumiHumanIDMapping_nuID"  
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>