Number of mapped keys for the maps in package illuminaRatv1.db

Description

illuminaRatv1MAPCOUNTS provides the "map count" (i.e. the count of mapped keys) for each map in package illuminaRatv1.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

  illuminaRatv1MAPCOUNTS
  mapnames <- names(illuminaRatv1MAPCOUNTS)
  illuminaRatv1MAPCOUNTS[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 illuminaRatv1.db
  checkMAPCOUNTS("illuminaRatv1.db")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(illuminaRatv1.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.Rn.eg.db


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/illuminaRatv1.db/illuminaRatv1MAPCOUNTS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaRatv1MAPCOUNTS
> ### Title: Number of mapped keys for the maps in package illuminaRatv1.db
> ### Aliases: illuminaRatv1MAPCOUNTS
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   illuminaRatv1MAPCOUNTS
       illuminaRatv1ACCNUM   illuminaRatv1ALIAS2PROBE 
                     18053                      25674 
          illuminaRatv1CHR    illuminaRatv1CHRLENGTHS 
                     15551                        953 
       illuminaRatv1CHRLOC     illuminaRatv1CHRLOCEND 
                     13997                      13997 
      illuminaRatv1ENSEMBL illuminaRatv1ENSEMBL2PROBE 
                     14512                      14172 
     illuminaRatv1ENTREZID        illuminaRatv1ENZYME 
                     15659                       1923 
 illuminaRatv1ENZYME2PROBE      illuminaRatv1GENENAME 
                       871                      15659 
           illuminaRatv1GO  illuminaRatv1GO2ALLPROBES 
                     13858                      18507 
     illuminaRatv1GO2PROBE          illuminaRatv1PATH 
                     14359                       5474 
   illuminaRatv1PATH2PROBE          illuminaRatv1PFAM 
                       225                      13593 
         illuminaRatv1PMID    illuminaRatv1PMID2PROBE 
                     12123                      80463 
      illuminaRatv1PROSITE        illuminaRatv1REFSEQ 
                     13593                      15659 
       illuminaRatv1SYMBOL       illuminaRatv1UNIGENE 
                     15659                      14252 
      illuminaRatv1UNIPROT 
                     13596 
>   mapnames <- names(illuminaRatv1MAPCOUNTS)
>   illuminaRatv1MAPCOUNTS[mapnames[1]]
illuminaRatv1ACCNUM 
              18053 
>   x <- get(mapnames[1])
>   sum(!is.na(as.list(x)))
[1] 18053
>   count.mappedkeys(x)   # much faster!
[1] 18053
> 
>   ## Check the "map count" of all the maps in package illuminaRatv1.db
>   checkMAPCOUNTS("illuminaRatv1.db")
Counting mapped keys for map illuminaRatv1ACCNUM:
  - length(map) = 23365
  - MAPCOUNTS["illuminaRatv1ACCNUM"] = 18053
  - count1 = 18053 (0.05 s)
  - count2 = 18053 (0.031 s)
  - count3 = 18053 (0.205 s)
Counting mapped keys for map illuminaRatv1ALIAS2PROBE:
  - length(map) = 58346
  - MAPCOUNTS["illuminaRatv1ALIAS2PROBE"] = 25674
  - count1 = 25465 (0.145 s)
Error in checkMAPCOUNTS("illuminaRatv1.db") : count1 and count0 differ
Execution halted