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

Description

lumiHumanAllMAPCOUNTS provides the "map count" (i.e. the count of mapped keys) for each map in package lumiHumanAll.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

  lumiHumanAllMAPCOUNTS
  mapnames <- names(lumiHumanAllMAPCOUNTS)
  lumiHumanAllMAPCOUNTS[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 lumiHumanAll.db
  checkMAPCOUNTS("lumiHumanAll.db")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> 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/lumiHumanAllMAPCOUNTS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lumiHumanAllMAPCOUNTS
> ### Title: Number of mapped keys for the maps in package lumiHumanAll.db
> ### Aliases: lumiHumanAllMAPCOUNTS
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   lumiHumanAllMAPCOUNTS
       lumiHumanAllACCNUM   lumiHumanAllALIAS2PROBE           lumiHumanAllCHR 
                   105521                     66274                     47248 
   lumiHumanAllCHRLENGTHS        lumiHumanAllCHRLOC     lumiHumanAllCHRLOCEND 
                       93                     46161                     46161 
      lumiHumanAllENSEMBL lumiHumanAllENSEMBL2PROBE      lumiHumanAllENTREZID 
                    46184                     23067                     47254 
       lumiHumanAllENZYME  lumiHumanAllENZYME2PROBE      lumiHumanAllGENENAME 
                     5621                       974                     47254 
           lumiHumanAllGO  lumiHumanAllGO2ALLPROBES      lumiHumanAllGO2PROBE 
                    41182                     17597                     13719 
          lumiHumanAllMAP          lumiHumanAllOMIM          lumiHumanAllPATH 
                    46738                     34131                     14363 
   lumiHumanAllPATH2PROBE          lumiHumanAllPFAM          lumiHumanAllPMID 
                      229                     43243                     46622 
   lumiHumanAllPMID2PROBE       lumiHumanAllPROSITE        lumiHumanAllREFSEQ 
                   390896                     43243                     47173 
       lumiHumanAllSYMBOL       lumiHumanAllUNIGENE       lumiHumanAllUNIPROT 
                    47254                     46080                     43297 
>   mapnames <- names(lumiHumanAllMAPCOUNTS)
>   lumiHumanAllMAPCOUNTS[mapnames[1]]
lumiHumanAllACCNUM 
            105521 
>   x <- get(mapnames[1])
>   sum(!is.na(as.list(x)))
[1] 105521
>   count.mappedkeys(x)   # much faster!
[1] 105521
> 
>   ## Check the "map count" of all the maps in package lumiHumanAll.db
>   checkMAPCOUNTS("lumiHumanAll.db")
Counting mapped keys for map lumiHumanAllACCNUM:
  - length(map) = 105521
  - MAPCOUNTS["lumiHumanAllACCNUM"] = 105521
  - count1 = 105521 (0.156 s)
  - count2 = 105521 (0.082 s)
  - count3 = 105521 (1.035 s)
Counting mapped keys for map lumiHumanAllALIAS2PROBE:
  - length(map) = 119263
  - MAPCOUNTS["lumiHumanAllALIAS2PROBE"] = 66274
  - count1 = 69858 (0.405 s)
Error in checkMAPCOUNTS("lumiHumanAll.db") : count1 and count0 differ
Execution halted