Map between Manufacturer Identifiers and Mendelian Inheritance in Man (MIM) identifiers

Description

lumiHumanAllOMIM is an R object that provides mappings between manufacturer identifiers and OMIM identifiers.

Details

Each manufacturer identifier is mapped to a vector of OMIM identifiers. The vector length may be one or longer, depending on how many OMIM identifiers the manufacturer identifier maps to. An NA is reported for any manufacturer identifier that cannot be mapped to an OMIM identifier at this time.

OMIM is based upon the book Mendelian Inheritance in Man (V. A. McKusick) and focuses primarily on inherited or heritable genetic diseases. It contains textual information, pictures, and reference information that can be searched using various terms, among which the MIM number is one.

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: 2013-Sep12

References

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene http://www3.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

Examples

        x <- lumiHumanAllOMIM
        # Get the probe identifiers that are mapped to a OMIM ID
        mapped_probes <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_probes])
        if(length(xx) > 0) {
          # Get the OMIM 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(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/lumiHumanAllOMIM.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lumiHumanAllOMIM
> ### Title: Map between Manufacturer Identifiers and Mendelian Inheritance
> ###   in Man (MIM) identifiers
> ### Aliases: lumiHumanAllOMIM
> ### Keywords: datasets
> 
> ### ** Examples
> 
>         x <- lumiHumanAllOMIM
>         # Get the probe identifiers that are mapped to a OMIM ID
>         mapped_probes <- mappedkeys(x)
>         # Convert to a list
>         xx <- as.list(x[mapped_probes])
>         if(length(xx) > 0) {
+           # Get the OMIM for the first five probes
+           xx[1:5]
+           # Get the first one
+           xx[[1]]
+         }
[1] "606115"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>