Map between Gene Ontology (GO) and Manufacturer Identifiers

Description

illuminaHumanv2BeadIDGO2PROBE is an R object that provides mappings between GO identifiers and manufacturer identifiers.

Details

Each GO term maps to a named vector of manufacturer identifiers. The name associated with each manufacturer identifier corresponds to the evidence code for that GO identifier. The evidence code indicates what kind of evidence supports the association between the GO and Entrez Gene identifiers. Evidence codes currently in use include:

IMP - inferred from mutant phenotype

IGI - inferred from genetic interaction

IPI - inferred from physical interaction

ISS - inferred from sequence similarity

IDA - inferred from direct assay

IEP - inferred from expression pattern

IEA - inferred from electronic annotation

TAS - traceable author statement

NAS - non-traceable author statement

ND - no biological data available

IC - inferred by curator

A GO identifier may be mapped to the same probe identifier more than once but the evidence code can be different. Mappings between Gene Ontology identifiers an Gene Ontology terms and other information are available in a separate data package named GO.

Mappings were based on data provided by:

Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA With a date stamp from the source of: 2010-Sep7

References

ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/

Examples

    # Convert to a list
    xx <- as.list(illuminaHumanv2BeadIDGO2PROBE)
    if(length(xx) > 0){
        # Get the probe identifiers for the top 2nd and 3nd GO identifiers
        goids <- xx[2:3]
        # Get the probe identifiers for the first element of goids
        goids[[1]]
        # Evidence code for the mappings
        names(goids[[1]])
    }

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)

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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(illuminaHumanv2BeadID.db)
Loading required package: AnnotationDbi
Loading required package: stats4
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

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

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

Loading required package: org.Hs.eg.db


illuminaHumanv2BeadID.db is an older package, and the package
  contributor no longer supports it. Please be advised that this
  package is now out of date and should not occur in future
  bioconductor releases.  For a more current package containing the
  same kind of data, please use the appropriate illumina_XXX_.db
  packages instead of the illumina_XXX_BeadID.db packages and make use
  of the new illumina_XXX_ARRAYADDRESS mapping to convert between
  BeadIDs and Illumina IDs.

*_XXX_ here refers to the species and version for this platform

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/illuminaHumanv2BeadID.db/illuminaHumanv2BeadIDGO2PROBE.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaHumanv2BeadIDGO2PROBE
> ### Title: Map between Gene Ontology (GO) and Manufacturer Identifiers
> ### Aliases: illuminaHumanv2BeadIDGO2PROBE
> ### Keywords: datasets
> 
> ### ** Examples
> 
>     # Convert to a list
>     xx <- as.list(illuminaHumanv2BeadIDGO2PROBE)
>     if(length(xx) > 0){
+         # Get the probe identifiers for the top 2nd and 3nd GO identifiers
+         goids <- xx[2:3]
+         # Get the probe identifiers for the first element of goids
+         goids[[1]]
+         # Evidence code for the mappings
+         names(goids[[1]])
+     }
[1] "IEP" "IBA"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>