Number of mapped keys for the maps in package lumiRatAll.db

Description

lumiRatAllMAPCOUNTS provides the "map count" (i.e. the count of mapped keys) for each map in package lumiRatAll.db.

Details

This "map count" information is precalculated and stored in the package annotation DB. This allows some quality control and is used by the checkMAPCOUNTS function defined in AnnotationDbi to compare and validate different methods (like count.mappedkeys(x) or sum(!is.na(as.list(x)))) for getting the "map count" of a given map.

See Also

mappedkeys, count.mappedkeys, checkMAPCOUNTS

Examples

  lumiRatAllMAPCOUNTS
  mapnames <- names(lumiRatAllMAPCOUNTS)
  lumiRatAllMAPCOUNTS[mapnames[1]]
  x <- get(mapnames[1])
  sum(!is.na(as.list(x)))
  count.mappedkeys(x)   # much faster!

  ## Check the "map count" of all the maps in package lumiRatAll.db
  checkMAPCOUNTS("lumiRatAll.db")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(lumiRatAll.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.Rn.eg.db


lumiRatAll.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/lumiRatAll.db/lumiRatAllMAPCOUNTS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lumiRatAllMAPCOUNTS
> ### Title: Number of mapped keys for the maps in package lumiRatAll.db
> ### Aliases: lumiRatAllMAPCOUNTS
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   lumiRatAllMAPCOUNTS
       lumiRatAllACCNUM   lumiRatAllALIAS2PROBE           lumiRatAllCHR 
                  22523                   18899                   10986 
   lumiRatAllCHRLENGTHS        lumiRatAllCHRLOC     lumiRatAllCHRLOCEND 
                   2739                    8460                    8460 
      lumiRatAllENSEMBL lumiRatAllENSEMBL2PROBE      lumiRatAllENTREZID 
                   9861                    9772                   11103 
       lumiRatAllENZYME  lumiRatAllENZYME2PROBE      lumiRatAllGENENAME 
                   1375                     721                   11103 
           lumiRatAllGO  lumiRatAllGO2ALLPROBES      lumiRatAllGO2PROBE 
                   9477                   15444                   11570 
         lumiRatAllPATH    lumiRatAllPATH2PROBE          lumiRatAllPFAM 
                   4233                     224                    8491 
         lumiRatAllPMID    lumiRatAllPMID2PROBE       lumiRatAllPROSITE 
                   8914                   67810                    8491 
       lumiRatAllREFSEQ        lumiRatAllSYMBOL       lumiRatAllUNIGENE 
                  11103                   11103                    9130 
      lumiRatAllUNIPROT 
                   8800 
>   mapnames <- names(lumiRatAllMAPCOUNTS)
>   lumiRatAllMAPCOUNTS[mapnames[1]]
lumiRatAllACCNUM 
           22523 
>   x <- get(mapnames[1])
>   sum(!is.na(as.list(x)))
[1] 22523
>   count.mappedkeys(x)   # much faster!
[1] 22523
> 
>   ## Check the "map count" of all the maps in package lumiRatAll.db
>   checkMAPCOUNTS("lumiRatAll.db")
Counting mapped keys for map lumiRatAllACCNUM:
  - length(map) = 22523
  - MAPCOUNTS["lumiRatAllACCNUM"] = 22523
  - count1 = 22523 (0.032 s)
  - count2 = 22523 (0.017 s)
  - count3 = 22523 (0.122 s)
Counting mapped keys for map lumiRatAllALIAS2PROBE:
  - length(map) = 58346
  - MAPCOUNTS["lumiRatAllALIAS2PROBE"] = 18899
  - count1 = 18657 (0.06 s)
Error in checkMAPCOUNTS("lumiRatAll.db") : count1 and count0 differ
Execution halted