Number of mapped keys for the maps in package illuminaMousev1p1.db

Description

illuminaMousev1p1MAPCOUNTS provides the "map count" (i.e. the count of mapped keys) for each map in package illuminaMousev1p1.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

  illuminaMousev1p1MAPCOUNTS
  mapnames <- names(illuminaMousev1p1MAPCOUNTS)
  illuminaMousev1p1MAPCOUNTS[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 illuminaMousev1p1.db
  checkMAPCOUNTS("illuminaMousev1p1.db")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(illuminaMousev1p1.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/illuminaMousev1p1.db/illuminaMousev1p1MAPCOUNTS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaMousev1p1MAPCOUNTS
> ### Title: Number of mapped keys for the maps in package
> ###   illuminaMousev1p1.db
> ### Aliases: illuminaMousev1p1MAPCOUNTS
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   illuminaMousev1p1MAPCOUNTS
       illuminaMousev1p1ACCNUM   illuminaMousev1p1ALIAS2PROBE 
                         32600                          73643 
          illuminaMousev1p1CHR    illuminaMousev1p1CHRLENGTHS 
                         30378                             66 
       illuminaMousev1p1CHRLOC     illuminaMousev1p1CHRLOCEND 
                         29904                          29904 
      illuminaMousev1p1ENSEMBL illuminaMousev1p1ENSEMBL2PROBE 
                         29390                          19477 
     illuminaMousev1p1ENTREZID        illuminaMousev1p1ENZYME 
                         30380                           3465 
 illuminaMousev1p1ENZYME2PROBE      illuminaMousev1p1GENENAME 
                           963                          30380 
           illuminaMousev1p1GO  illuminaMousev1p1GO2ALLPROBES 
                         29345                          19813 
     illuminaMousev1p1GO2PROBE           illuminaMousev1p1MGI 
                         15782                          30364 
    illuminaMousev1p1MGI2PROBE          illuminaMousev1p1PATH 
                         20223                           9494 
   illuminaMousev1p1PATH2PROBE          illuminaMousev1p1PFAM 
                           225                          28766 
         illuminaMousev1p1PMID    illuminaMousev1p1PMID2PROBE 
                         30224                         230330 
      illuminaMousev1p1PROSITE        illuminaMousev1p1REFSEQ 
                         28766                          30380 
       illuminaMousev1p1SYMBOL       illuminaMousev1p1UNIGENE 
                         30380                          30189 
      illuminaMousev1p1UNIPROT 
                         28765 
>   mapnames <- names(illuminaMousev1p1MAPCOUNTS)
>   illuminaMousev1p1MAPCOUNTS[mapnames[1]]
illuminaMousev1p1ACCNUM 
                  32600 
>   x <- get(mapnames[1])
>   sum(!is.na(as.list(x)))
[1] 32600
>   count.mappedkeys(x)   # much faster!
[1] 32600
> 
>   ## Check the "map count" of all the maps in package illuminaMousev1p1.db
>   checkMAPCOUNTS("illuminaMousev1p1.db")
Counting mapped keys for map illuminaMousev1p1ACCNUM:
  - length(map) = 47522
  - MAPCOUNTS["illuminaMousev1p1ACCNUM"] = 32600
  - count1 = 32600 (0.052 s)
  - count2 = 32600 (0.038 s)
  - count3 = 32600 (0.299 s)
Counting mapped keys for map illuminaMousev1p1ALIAS2PROBE:
  - length(map) = 143708
  - MAPCOUNTS["illuminaMousev1p1ALIAS2PROBE"] = 73643
  - count1 = 74056 (0.319 s)
Error in checkMAPCOUNTS("illuminaMousev1p1.db") : 
  count1 and count0 differ
Execution halted