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

Description

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

  mirbaseMAPCOUNTS
  mapnames <- names(mirbaseMAPCOUNTS)
  mirbaseMAPCOUNTS[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 mirbase.db
  checkMAPCOUNTS("mirbase.db")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(mirbase.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

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mirbase.db/mirbaseMAPCOUNTS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mirbaseMAPCOUNTS
> ### Title: Number of mapped keys for the maps in package mirbase.db
> ### Aliases: mirbaseMAPCOUNTS
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   mirbaseMAPCOUNTS
        mirbaseCHR      mirbaseCHRLOC   mirbaseCHRLOCEND     mirbaseCLUSTER 
             17312              17312              17312              15365 
    mirbaseCOMMENT     mirbaseCONTEXT mirbaseDESCRIPTION      mirbaseFAMILY 
             21264               5500              21264              15588 
    mirbaseHAIRPIN      mirbaseID2ACC  mirbaseID2SPECIES       mirbaseLINKS 
             21264              21264              21264               7991 
     mirbaseMATURE         mirbaseMFE        mirbasePMID    mirbaseSEQUENCE 
             21264              21264              20716              21264 
    mirbaseSPECIES 
               193 
>   mapnames <- names(mirbaseMAPCOUNTS)
>   mirbaseMAPCOUNTS[mapnames[1]]
mirbaseCHR 
     17312 
>   x <- get(mapnames[1])
>   sum(!is.na(as.list(x)))
[1] 17312
>   count.mappedkeys(x)   # much faster!
[1] 17312
> 
>   ## Check the "map count" of all the maps in package mirbase.db
>   checkMAPCOUNTS("mirbase.db")
Counting mapped keys for map mirbaseCHR:
  - length(map) = 21264
  - MAPCOUNTS["mirbaseCHR"] = 17312
  - count1 = 17312 (0.033 s)
  - count2 = 17312 (0.039 s)
  - count3 = 17312 (0.111 s)
Counting mapped keys for map mirbaseCHRLOC:
  - length(map) = 21264
  - MAPCOUNTS["mirbaseCHRLOC"] = 17312
  - count1 = 17312 (0.034 s)
  - count2 = 17312 (0.038 s)
  - count3 = 17312 (0.121 s)
Counting mapped keys for map mirbaseCHRLOCEND:
  - length(map) = 21264
  - MAPCOUNTS["mirbaseCHRLOCEND"] = 17312
  - count1 = 17312 (0.034 s)
  - count2 = 17312 (0.039 s)
  - count3 = 17312 (0.12 s)
Counting mapped keys for map mirbaseCLUSTER:
  - length(map) = 15365
  - MAPCOUNTS["mirbaseCLUSTER"] = 15365
  - count1 = 15365 (0.049 s)
  - count2 = 15365 (0.072 s)
  - count3 = 15365 (0.229 s)
Counting mapped keys for map mirbaseCOMMENT:
  - length(map) = 21264
  - MAPCOUNTS["mirbaseCOMMENT"] = 21264
  - count1 = 21264 (0.04 s)
  - count2 = 21264 (0.074 s)
  - count3 = 21264 (0.207 s)
Counting mapped keys for map mirbaseCONTEXT:
  - length(map) = 21264
  - MAPCOUNTS["mirbaseCONTEXT"] = 5500
  - count1 = 5500 (0.04 s)
  - count2 = 5500 (0.043 s)
  - count3 = 5500 (2.725 s)
Counting mapped keys for map mirbaseDESCRIPTION:
  - length(map) = 21264
  - MAPCOUNTS["mirbaseDESCRIPTION"] = 21264
  - count1 = 21264 (0.038 s)
  - count2 = 21264 (0.046 s)
  - count3 = 21264 (0.121 s)
Counting mapped keys for map mirbaseFAMILY:
  - length(map) = 21264
  - MAPCOUNTS["mirbaseFAMILY"] = 15588
  - count1 = 15588 (0.039 s)
  - count2 = 15588 (0.043 s)
  - count3 = 15588 (0.117 s)
Counting mapped keys for map mirbaseHAIRPIN:
  - length(map) = 21264
  - MAPCOUNTS["mirbaseHAIRPIN"] = 21264
  - count1 = 21264 (0.039 s)
  - count2 = 21264 (0.046 s)
  - count3 = 21264 (0.196 s)
Counting mapped keys for map mirbaseID2ACC:
  - length(map) = 21264
  - MAPCOUNTS["mirbaseID2ACC"] = 21264
  - count1 = 21264 (0.038 s)
  - count2 = 21264 (0.045 s)
  - count3 = 21264 (0.117 s)
Counting mapped keys for map mirbaseID2SPECIES:
  - length(map) = 21264
  - MAPCOUNTS["mirbaseID2SPECIES"] = 21264
  - count1 = 21264 (0.038 s)
  - count2 = 21264 (0.044 s)
  - count3 = 21264 (0.109 s)
Counting mapped keys for map mirbaseLINKS:
  - length(map) = 21264
  - MAPCOUNTS["mirbaseLINKS"] = 7991
  - count1 = 7991 (0.036 s)
  - count2 = 7991 (0.022 s)
  - count3 = 7991 (2.411 s)
Counting mapped keys for map mirbaseMATURE:
  - length(map) = 21264
  - MAPCOUNTS["mirbaseMATURE"] = 21264
  - count1 = 21264 (0.098 s)
  - count2 = 21264 (0.095 s)
  - count3 = 21264 (9.21 s)
Counting mapped keys for map mirbaseMFE:
  - length(map) = 21264
  - MAPCOUNTS["mirbaseMFE"] = 21264
  - count1 = 21264 (0.038 s)
  - count2 = 21264 (0.045 s)
  - count3 = 21264 (0.113 s)
Counting mapped keys for map mirbasePMID:
  - length(map) = 21264
  - MAPCOUNTS["mirbasePMID"] = 20716
  - count1 = 20716 (0.052 s)
  - count2 = 20716 (0.053 s)
  - count3 = 20716 (7.735 s)
Counting mapped keys for map mirbaseSEQUENCE:
  - length(map) = 21264
  - MAPCOUNTS["mirbaseSEQUENCE"] = 21264
  - count1 = 21264 (0.044 s)
  - count2 = 21264 (0.052 s)
  - count3 = 21264 (0.133 s)
Counting mapped keys for map mirbaseSPECIES:
  - length(map) = 193
  - MAPCOUNTS["mirbaseSPECIES"] = 193
  - count1 = 193 (0.002 s)
  - count2 = 193 (0.003 s)
  - count3 = 193 (0.004 s)
There were 50 or more warnings (use warnings() to see the first 50)
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> dev.off()
null device 
          1 
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