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

Description

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

  lumiMouseAllMAPCOUNTS
  mapnames <- names(lumiMouseAllMAPCOUNTS)
  lumiMouseAllMAPCOUNTS[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 lumiMouseAll.db
  checkMAPCOUNTS("lumiMouseAll.db")

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(lumiMouseAll.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


lumiMouseAll.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/lumiMouseAll.db/lumiMouseAllMAPCOUNTS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lumiMouseAllMAPCOUNTS
> ### Title: Number of mapped keys for the maps in package lumiMouseAll.db
> ### Aliases: lumiMouseAllMAPCOUNTS
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   lumiMouseAllMAPCOUNTS
       lumiMouseAllACCNUM   lumiMouseAllALIAS2PROBE           lumiMouseAllCHR 
                    54437                     72223                     43454 
   lumiMouseAllCHRLENGTHS        lumiMouseAllCHRLOC     lumiMouseAllCHRLOCEND 
                       66                     41952                     41952 
      lumiMouseAllENSEMBL lumiMouseAllENSEMBL2PROBE      lumiMouseAllENTREZID 
                    41960                     18903                     43476 
       lumiMouseAllENZYME  lumiMouseAllENZYME2PROBE      lumiMouseAllGENENAME 
                     5250                       959                     43476 
           lumiMouseAllGO  lumiMouseAllGO2ALLPROBES      lumiMouseAllGO2PROBE 
                    42511                     17222                     13473 
          lumiMouseAllMGI     lumiMouseAllMGI2PROBE          lumiMouseAllPATH 
                    43404                     19851                     14022 
   lumiMouseAllPATH2PROBE          lumiMouseAllPFAM          lumiMouseAllPMID 
                      225                     41034                     43137 
   lumiMouseAllPMID2PROBE       lumiMouseAllPROSITE        lumiMouseAllREFSEQ 
                   205328                     41034                     43246 
       lumiMouseAllSYMBOL       lumiMouseAllUNIGENE       lumiMouseAllUNIPROT 
                    43476                     42918                     41476 
>   mapnames <- names(lumiMouseAllMAPCOUNTS)
>   lumiMouseAllMAPCOUNTS[mapnames[1]]
lumiMouseAllACCNUM 
             54437 
>   x <- get(mapnames[1])
>   sum(!is.na(as.list(x)))
[1] 54437
>   count.mappedkeys(x)   # much faster!
[1] 54437
> 
>   ## Check the "map count" of all the maps in package lumiMouseAll.db
>   checkMAPCOUNTS("lumiMouseAll.db")
Counting mapped keys for map lumiMouseAllACCNUM:
  - length(map) = 60385
  - MAPCOUNTS["lumiMouseAllACCNUM"] = 54437
  - count1 = 54437 (0.077 s)
  - count2 = 54437 (0.047 s)
  - count3 = 54437 (0.414 s)
Counting mapped keys for map lumiMouseAllALIAS2PROBE:
  - length(map) = 143708
  - MAPCOUNTS["lumiMouseAllALIAS2PROBE"] = 72223
  - count1 = 72684 (0.404 s)
Error in checkMAPCOUNTS("lumiMouseAll.db") : count1 and count0 differ
Execution halted