Number of mapped keys for the maps in package illuminaMousev1.db

Description

illuminaMousev1MAPCOUNTS provides the "map count" (i.e. the count of mapped keys) for each map in package illuminaMousev1.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

  illuminaMousev1MAPCOUNTS
  mapnames <- names(illuminaMousev1MAPCOUNTS)
  illuminaMousev1MAPCOUNTS[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 illuminaMousev1.db
  checkMAPCOUNTS("illuminaMousev1.db")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(illuminaMousev1.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/illuminaMousev1.db/illuminaMousev1MAPCOUNTS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaMousev1MAPCOUNTS
> ### Title: Number of mapped keys for the maps in package illuminaMousev1.db
> ### Aliases: illuminaMousev1MAPCOUNTS
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   illuminaMousev1MAPCOUNTS
       illuminaMousev1ACCNUM   illuminaMousev1ALIAS2PROBE 
                       32091                        72491 
          illuminaMousev1CHR    illuminaMousev1CHRLENGTHS 
                       29898                           66 
       illuminaMousev1CHRLOC     illuminaMousev1CHRLOCEND 
                       29439                        29439 
      illuminaMousev1ENSEMBL illuminaMousev1ENSEMBL2PROBE 
                       28928                        19078 
     illuminaMousev1ENTREZID        illuminaMousev1ENZYME 
                       29900                         3433 
 illuminaMousev1ENZYME2PROBE      illuminaMousev1GENENAME 
                         958                        29900 
           illuminaMousev1GO  illuminaMousev1GO2ALLPROBES 
                       28890                        19783 
     illuminaMousev1GO2PROBE           illuminaMousev1MGI 
                       15743                        29887 
    illuminaMousev1MGI2PROBE          illuminaMousev1PATH 
                       19807                         9366 
   illuminaMousev1PATH2PROBE          illuminaMousev1PFAM 
                         225                        28319 
         illuminaMousev1PMID    illuminaMousev1PMID2PROBE 
                       29746                       229193 
      illuminaMousev1PROSITE        illuminaMousev1REFSEQ 
                       28319                        29900 
       illuminaMousev1SYMBOL       illuminaMousev1UNIGENE 
                       29900                        29708 
      illuminaMousev1UNIPROT 
                       28318 
>   mapnames <- names(illuminaMousev1MAPCOUNTS)
>   illuminaMousev1MAPCOUNTS[mapnames[1]]
illuminaMousev1ACCNUM 
                32091 
>   x <- get(mapnames[1])
>   sum(!is.na(as.list(x)))
[1] 32091
>   count.mappedkeys(x)   # much faster!
[1] 32091
> 
>   ## Check the "map count" of all the maps in package illuminaMousev1.db
>   checkMAPCOUNTS("illuminaMousev1.db")
Counting mapped keys for map illuminaMousev1ACCNUM:
  - length(map) = 45988
  - MAPCOUNTS["illuminaMousev1ACCNUM"] = 32091
  - count1 = 32091 (0.061 s)
  - count2 = 32091 (0.041 s)
  - count3 = 32091 (0.316 s)
Counting mapped keys for map illuminaMousev1ALIAS2PROBE:
  - length(map) = 143708
  - MAPCOUNTS["illuminaMousev1ALIAS2PROBE"] = 72491
  - count1 = 72900 (0.301 s)
Error in checkMAPCOUNTS("illuminaMousev1.db") : count1 and count0 differ
Execution halted