Number of mapped keys for the maps in package illuminaMousev2.db

Description

illuminaMousev2MAPCOUNTS provides the "map count" (i.e. the count of mapped keys) for each map in package illuminaMousev2.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

  illuminaMousev2MAPCOUNTS
  mapnames <- names(illuminaMousev2MAPCOUNTS)
  illuminaMousev2MAPCOUNTS[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 illuminaMousev2.db
  checkMAPCOUNTS("illuminaMousev2.db")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(illuminaMousev2.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/illuminaMousev2.db/illuminaMousev2MAPCOUNTS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaMousev2MAPCOUNTS
> ### Title: Number of mapped keys for the maps in package illuminaMousev2.db
> ### Aliases: illuminaMousev2MAPCOUNTS
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   illuminaMousev2MAPCOUNTS
       illuminaMousev2ACCNUM   illuminaMousev2ALIAS2PROBE 
                       35970                        73613 
          illuminaMousev2CHR    illuminaMousev2CHRLENGTHS 
                       33843                           66 
       illuminaMousev2CHRLOC     illuminaMousev2CHRLOCEND 
                       33428                        33428 
      illuminaMousev2ENSEMBL illuminaMousev2ENSEMBL2PROBE 
                       33014                        19449 
     illuminaMousev2ENTREZID        illuminaMousev2ENZYME 
                       33845                         3965 
 illuminaMousev2ENZYME2PROBE      illuminaMousev2GENENAME 
                         964                        33845 
           illuminaMousev2GO  illuminaMousev2GO2ALLPROBES 
                       33062                        19802 
     illuminaMousev2GO2PROBE           illuminaMousev2MGI 
                       15768                        33826 
    illuminaMousev2MGI2PROBE          illuminaMousev2PATH 
                       20040                        10730 
   illuminaMousev2PATH2PROBE          illuminaMousev2PFAM 
                         225                        32629 
         illuminaMousev2PMID    illuminaMousev2PMID2PROBE 
                       33682                       230353 
      illuminaMousev2PROSITE        illuminaMousev2REFSEQ 
                       32629                        33845 
       illuminaMousev2SYMBOL       illuminaMousev2UNIGENE 
                       33845                        33655 
      illuminaMousev2UNIPROT 
                       32628 
>   mapnames <- names(illuminaMousev2MAPCOUNTS)
>   illuminaMousev2MAPCOUNTS[mapnames[1]]
illuminaMousev2ACCNUM 
                35970 
>   x <- get(mapnames[1])
>   sum(!is.na(as.list(x)))
[1] 35970
>   count.mappedkeys(x)   # much faster!
[1] 35970
> 
>   ## Check the "map count" of all the maps in package illuminaMousev2.db
>   checkMAPCOUNTS("illuminaMousev2.db")
Counting mapped keys for map illuminaMousev2ACCNUM:
  - length(map) = 46237
  - MAPCOUNTS["illuminaMousev2ACCNUM"] = 35970
  - count1 = 35970 (0.107 s)
  - count2 = 35970 (0.063 s)
  - count3 = 35970 (0.493 s)
Counting mapped keys for map illuminaMousev2ALIAS2PROBE:
  - length(map) = 143708
  - MAPCOUNTS["illuminaMousev2ALIAS2PROBE"] = 73613
  - count1 = 74019 (0.537 s)
Error in checkMAPCOUNTS("illuminaMousev2.db") : count1 and count0 differ
Execution halted