Number of mapped keys for the maps in package m20kcod.db

Description

m20kcodMAPCOUNTS provides the "map count" (i.e. the count of mapped keys) for each map in package m20kcod.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

  m20kcodMAPCOUNTS
  mapnames <- names(m20kcodMAPCOUNTS)
  m20kcodMAPCOUNTS[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 m20kcod.db
  checkMAPCOUNTS("m20kcod.db")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(m20kcod.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.Mm.eg.db


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/m20kcod.db/m20kcodMAPCOUNTS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: m20kcodMAPCOUNTS
> ### Title: Number of mapped keys for the maps in package m20kcod.db
> ### Aliases: m20kcodMAPCOUNTS
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   m20kcodMAPCOUNTS
       m20kcodACCNUM   m20kcodALIAS2PROBE           m20kcodCHR 
               19793                54145                16290 
   m20kcodCHRLENGTHS        m20kcodCHRLOC     m20kcodCHRLOCEND 
                  66                15737                15737 
      m20kcodENSEMBL m20kcodENSEMBL2PROBE      m20kcodENTREZID 
               15600                13458                16300 
       m20kcodENZYME  m20kcodENZYME2PROBE      m20kcodGENENAME 
                2042                  848                16300 
           m20kcodGO  m20kcodGO2ALLPROBES      m20kcodGO2PROBE 
               15658                19734                15399 
          m20kcodMGI     m20kcodMGI2PROBE          m20kcodPATH 
               16276                14033                 5350 
   m20kcodPATH2PROBE          m20kcodPFAM          m20kcodPMID 
                 225                15387                16280 
   m20kcodPMID2PROBE       m20kcodPROSITE        m20kcodREFSEQ 
              217620                15387                16010 
       m20kcodSYMBOL       m20kcodUNIGENE       m20kcodUNIPROT 
               16300                16148                15387 
>   mapnames <- names(m20kcodMAPCOUNTS)
>   m20kcodMAPCOUNTS[mapnames[1]]
m20kcodACCNUM 
        19793 
>   x <- get(mapnames[1])
>   sum(!is.na(as.list(x)))
[1] 19793
>   count.mappedkeys(x)   # much faster!
[1] 19793
> 
>   ## Check the "map count" of all the maps in package m20kcod.db
>   checkMAPCOUNTS("m20kcod.db")
Counting mapped keys for map m20kcodACCNUM:
  - length(map) = 19874
  - MAPCOUNTS["m20kcodACCNUM"] = 19793
  - count1 = 19793 (0.052 s)
  - count2 = 19793 (0.026 s)
  - count3 = 19793 (0.131 s)
Counting mapped keys for map m20kcodALIAS2PROBE:
  - length(map) = 143708
  - MAPCOUNTS["m20kcodALIAS2PROBE"] = 54145
  - count1 = 54291 (0.169 s)
Error in checkMAPCOUNTS("m20kcod.db") : count1 and count0 differ
Execution halted