Map Manufacturer identifiers to Accession Numbers

Description

illuminaHumanv2BeadIDACCNUM is an R object that contains mappings between a manufacturer's identifiers and manufacturers accessions.

Details

For chip packages such as this, the ACCNUM mapping comes directly from the manufacturer. This is different from other mappings which are mapped onto the probes via an Entrez Gene identifier.

Each manufacturer identifier maps to a vector containing a GenBank accession number.

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

Examples

        x <- illuminaHumanv2BeadIDACCNUM
        # Get the probe identifiers that are mapped to an ACCNUM
        mapped_probes <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_probes])
        if(length(xx) > 0) {
          # Get the ACCNUM for the first five probes
          xx[1:5]
          # Get the first one
          xx[[1]]
        }

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> 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/illuminaHumanv2BeadIDACCNUM.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaHumanv2BeadIDACCNUM
> ### Title: Map Manufacturer identifiers to Accession Numbers
> ### Aliases: illuminaHumanv2BeadIDACCNUM
> ### Keywords: datasets
> 
> ### ** Examples
> 
>         x <- illuminaHumanv2BeadIDACCNUM
>         # Get the probe identifiers that are mapped to an ACCNUM
>         mapped_probes <- mappedkeys(x)
>         # Convert to a list
>         xx <- as.list(x[mapped_probes])
>         if(length(xx) > 0) {
+           # Get the ACCNUM for the first five probes
+           xx[1:5]
+           # Get the first one
+           xx[[1]]
+         }
[1] "NM_174978"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>