Number of mapped keys for the maps in package illuminaHumanv2.db

Description

illuminaHumanv2MAPCOUNTS provides the "map count" (i.e. the count of mapped keys) for each map in package illuminaHumanv2.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

  illuminaHumanv2MAPCOUNTS
  mapnames <- names(illuminaHumanv2MAPCOUNTS)
  illuminaHumanv2MAPCOUNTS[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 illuminaHumanv2.db
  checkMAPCOUNTS("illuminaHumanv2.db")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(illuminaHumanv2.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.Hs.eg.db


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/illuminaHumanv2.db/illuminaHumanv2MAPCOUNTS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaHumanv2MAPCOUNTS
> ### Title: Number of mapped keys for the maps in package illuminaHumanv2.db
> ### Aliases: illuminaHumanv2MAPCOUNTS
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   illuminaHumanv2MAPCOUNTS
       illuminaHumanv2ACCNUM   illuminaHumanv2ALIAS2PROBE 
                       26691                        62445 
          illuminaHumanv2CHR    illuminaHumanv2CHRLENGTHS 
                       24555                           93 
       illuminaHumanv2CHRLOC     illuminaHumanv2CHRLOCEND 
                       24366                        24366 
      illuminaHumanv2ENSEMBL illuminaHumanv2ENSEMBL2PROBE 
                       24198                        20703 
     illuminaHumanv2ENTREZID        illuminaHumanv2ENZYME 
                       24555                         2897 
 illuminaHumanv2ENZYME2PROBE      illuminaHumanv2GENENAME 
                         965                        24555 
           illuminaHumanv2GO  illuminaHumanv2GO2ALLPROBES 
                       22263                        19449 
     illuminaHumanv2GO2PROBE           illuminaHumanv2MAP 
                       15179                        24388 
         illuminaHumanv2OMIM          illuminaHumanv2PATH 
                       18008                         7561 
   illuminaHumanv2PATH2PROBE          illuminaHumanv2PFAM 
                         229                        22888 
         illuminaHumanv2PMID    illuminaHumanv2PMID2PROBE 
                       24338                       437568 
      illuminaHumanv2PROSITE        illuminaHumanv2REFSEQ 
                       22888                        24555 
       illuminaHumanv2SYMBOL       illuminaHumanv2UNIGENE 
                       24555                        24446 
      illuminaHumanv2UNIPROT 
                       22878 
>   mapnames <- names(illuminaHumanv2MAPCOUNTS)
>   illuminaHumanv2MAPCOUNTS[mapnames[1]]
illuminaHumanv2ACCNUM 
                26691 
>   x <- get(mapnames[1])
>   sum(!is.na(as.list(x)))
[1] 26691
>   count.mappedkeys(x)   # much faster!
[1] 26691
> 
>   ## Check the "map count" of all the maps in package illuminaHumanv2.db
>   checkMAPCOUNTS("illuminaHumanv2.db")
Counting mapped keys for map illuminaHumanv2ACCNUM:
  - length(map) = 49481
  - MAPCOUNTS["illuminaHumanv2ACCNUM"] = 26691
  - count1 = 26691 (0.093 s)
  - count2 = 26691 (0.064 s)
  - count3 = 26691 (0.496 s)
Counting mapped keys for map illuminaHumanv2ALIAS2PROBE:
  - length(map) = 119263
  - MAPCOUNTS["illuminaHumanv2ALIAS2PROBE"] = 62445
  - count1 = 63486 (0.382 s)
Error in checkMAPCOUNTS("illuminaHumanv2.db") : count1 and count0 differ
Execution halted