Map Manufacturer IDs to Pfam IDs

Description

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

Details

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

If the Pfam 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 Pfam identifier in the entry.

If the Pfam 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: Uniprot http://www.UniProt.org/ With a date stamp from the source of: Mon Sep 16 12:05:19 2013

Examples

        x <- lumiHumanAllPFAM
        # Get the probe identifiers that are mapped to any Pfam ID
        mapped_probes <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_probes])
        # randomly display 10 probes
        sample(xx, 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)

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(lumiHumanAll.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


lumiHumanAll.db is using or is likely to need access to special nuID
  identifiers.  Users can learn about these identifiers from vignette
  documentation provided with the lumi package.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lumiHumanAll.db/lumiHumanAllPFAM.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lumiHumanAllPFAM
> ### Title: Map Manufacturer IDs to Pfam IDs
> ### Aliases: lumiHumanAllPFAM
> ### Keywords: datasets
> 
> ### ** Examples
> 
>         x <- lumiHumanAllPFAM
>         # Get the probe identifiers that are mapped to any Pfam 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