Map between Manufacturer Identifiers and RefSeq Identifiers

Description

illuminaHumanv2BeadIDREFSEQ is an R object that provides mappings between manufacturer identifiers and RefSeq identifiers.

Details

Each manufacturer identifier is mapped to a named vector of RefSeq identifiers. The name represents the manufacturer identifier and the vector contains all RefSeq identifiers that can be mapped to that manufacturer identifier. The length of the vector may be one or greater, depending on how many RefSeq identifiers a given manufacturer identifier can be mapped to. An NA is reported for any manufacturer identifier that cannot be mapped to a RefSeq identifier at this time.

RefSeq identifiers differ in format according to the type of record the identifiers are for as shown below:

NG_XXXXX: RefSeq accessions for genomic region (nucleotide) records

NM_XXXXX: RefSeq accessions for mRNA records

NC_XXXXX: RefSeq accessions for chromosome records

NP_XXXXX: RefSeq accessions for protein records

XR_XXXXX: RefSeq accessions for model RNAs that are not associated with protein products

XM_XXXXX: RefSeq accessions for model mRNA records

XP_XXXXX: RefSeq accessions for model protein records

Where XXXXX is a sequence of integers.

NCBI http://www.ncbi.nlm.nih.gov/RefSeq/ allows users to query the RefSeq database using RefSeq identifiers.

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

http://www.ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov/RefSeq/

Examples

        x <- illuminaHumanv2BeadIDREFSEQ
        # Get the probe identifiers that are mapped to any RefSeq ID
        mapped_probes <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_probes])
        if(length(xx) > 0) {
          # Get the REFSEQ 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(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/illuminaHumanv2BeadIDREFSEQ.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaHumanv2BeadIDREFSEQ
> ### Title: Map between Manufacturer Identifiers and RefSeq Identifiers
> ### Aliases: illuminaHumanv2BeadIDREFSEQ
> ### Keywords: datasets
> 
> ### ** Examples
> 
>         x <- illuminaHumanv2BeadIDREFSEQ
>         # Get the probe identifiers that are mapped to any RefSeq ID
>         mapped_probes <- mappedkeys(x)
>         # Convert to a list
>         xx <- as.list(x[mapped_probes])
>         if(length(xx) > 0) {
+           # Get the REFSEQ for the first five probes
+           xx[1:5]
+           # Get the first one
+           xx[[1]]
+         }
 [1] "NM_174978"    "NP_777638"    "XM_011536689" "XM_011536690" "XM_011536691"
 [6] "XM_011536692" "XM_011536693" "XM_011536694" "XM_011536695" "XM_011536696"
[11] "XM_011536697" "XM_011536698" "XM_011536699" "XM_011536700" "XM_011536701"
[16] "XM_011536702" "XM_011536703" "XM_011536704" "XP_011534991" "XP_011534992"
[21] "XP_011534993" "XP_011534994" "XP_011534995" "XP_011534996" "XP_011534997"
[26] "XP_011534998" "XP_011534999" "XP_011535000" "XP_011535001" "XP_011535002"
[31] "XP_011535003" "XP_011535004" "XP_011535005" "XP_011535006" "XR_943417"   
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>