Map Manufacturer identifiers to Accession Numbers

Description

illuminaMousev2ACCNUM 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: 2015-Mar17

Examples

        x <- illuminaMousev2ACCNUM
        # 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"
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.
You are welcome to redistribute it under certain conditions.
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(illuminaMousev2.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.Mm.eg.db


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/illuminaMousev2.db/illuminaMousev2ACCNUM.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaMousev2ACCNUM
> ### Title: Map Manufacturer identifiers to Accession Numbers
> ### Aliases: illuminaMousev2ACCNUM
> ### Keywords: datasets
> 
> ### ** Examples
> 
>         x <- illuminaMousev2ACCNUM
>         # 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_011913"    "XM_003086130"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>