Map Manufacturer IDs to PROSITE ID

Description

illuminaHumanv2BeadIDPROSITE is an R object that provides mappings between a manufacturer identifier and the associated PROSITE identifiers.

Details

Each manufacturer identifier maps to a named vector of PROSITE identifiers. The name for each PROSITE identifier is the IPI accession numbe where this PROSITE identifier is found.

If the PROSITE is a named NA, it means that the associated Entrez Gene id of this manufacturer identifier is found in an IPI entry of the IPI database, but there is no PROSITE identifier in the entry.

If the PROSITE is a non-named NA, it means that the associated Entrez Gene id of this manufacturer identifier is not found in any IPI entry of the IPI database.

Mappings were based on data provided by: The International Protein Index ftp://ftp.ebi.ac.uk/pub/databases/IPI/current With a date stamp from the source of: 2010-Aug19

References

Kersey P. J., Duarte J., Williams A., Karavidopoulou Y., Birney E., Apweiler R. The International Protein Index: An integrated database for proteomics experiments. Proteomics 4(7): 1985-1988 (2004) http://www.ebi.ac.uk/IPI/IPIhelp.html

Examples

	        x <- illuminaHumanv2BeadIDPROSITE
        # Get the probe identifiers that are mapped to any PROSITE ID
        mapped_probes <- mappedkeys(x)
        # Convert to a list
        xxx <- as.list(x[mapped_probes])
        # randomly display 10 probes
        xxx[sample(1:length(xxx), 10)]

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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> 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/illuminaHumanv2BeadIDPROSITE.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaHumanv2BeadIDPROSITE
> ### Title: Map Manufacturer IDs to PROSITE ID
> ### Aliases: illuminaHumanv2BeadIDPROSITE
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 	        x <- illuminaHumanv2BeadIDPROSITE
>         # Get the probe identifiers that are mapped to any PROSITE ID
>         mapped_probes <- mappedkeys(x)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'mappedkeys' for signature '"NULL"'
Calls: mappedkeys -> <Anonymous>
Execution halted