Number of mapped keys for the maps in package org.At.tair.db

Description

org.At.tairMAPCOUNTS provides the "map count" (i.e. the count of mapped keys) for each map in package org.At.tair.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

• AnnotationDb-class for use of the select() interface.

Examples

## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.

## Bimap interface:
org.At.tairMAPCOUNTS
mapnames <- names(org.At.tairMAPCOUNTS)
org.At.tairMAPCOUNTS[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 org.At.tair.db
checkMAPCOUNTS("org.At.tair.db")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(org.At.tair.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/org.At.tair.db/org.At.tairMAPCOUNTS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: org.At.tairMAPCOUNTS
> ### Title: Number of mapped keys for the maps in package org.At.tair.db
> ### Aliases: org.At.tairMAPCOUNTS
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## select() interface:
> ## Objects in this package can be accessed using the select() interface
> ## from the AnnotationDbi package. See ?select for details.
> 
> ## Bimap interface:
> org.At.tairMAPCOUNTS
      org.At.tairARACYC org.At.tairARACYCENZYME          org.At.tairCHR 
                    567                    2710                   27416 
  org.At.tairCHRLENGTHS       org.At.tairCHRLOC    org.At.tairCHRLOCEND 
                      7                   27205                   27205 
      org.At.tairENZYME  org.At.tairENZYME2TAIR     org.At.tairGENENAME 
                   2121                     723                    7804 
          org.At.tairGO  org.At.tairGO2ALLTAIRS      org.At.tairGO2TAIR 
                  26863                    7436                    4890 
        org.At.tairPATH    org.At.tairPATH2TAIR         org.At.tairPMID 
                   3450                     123                   22530 
   org.At.tairPMID2TAIR       org.At.tairREFSEQ  org.At.tairREFSEQ2TAIR 
                  22060                   27205                   70352 
      org.At.tairSYMBOL 
                  11114 
> mapnames <- names(org.At.tairMAPCOUNTS)
> org.At.tairMAPCOUNTS[mapnames[1]]
org.At.tairARACYC 
              567 
> x <- get(mapnames[1])
> sum(!is.na(as.list(x)))
[1] 567
> count.mappedkeys(x)   # much faster!
[1] 567
> 
> ## Check the "map count" of all the maps in package org.At.tair.db
> checkMAPCOUNTS("org.At.tair.db")
Counting mapped keys for map org.At.tairARACYC:
  - length(map) = 567
  - MAPCOUNTS["org.At.tairARACYC"] = 567
  - count1 = 567 (0.012 s)
  - count2 = 567 (0.011 s)
  - count3 = 567 (0.015 s)
Counting mapped keys for map org.At.tairARACYCENZYME:
  - length(map) = 27416
  - MAPCOUNTS["org.At.tairARACYCENZYME"] = 2710
  - count1 = 2710 (0.011 s)
  - count2 = 2710 (0.01 s)
  - count3 = 2710 (0.214 s)
Counting mapped keys for map org.At.tairCHR:
  - length(map) = 27416
  - MAPCOUNTS["org.At.tairCHR"] = 27416
  - count1 = 27416 (0.079 s)
  - count2 = 27416 (0.061 s)
  - count3 = 27416 (0.245 s)
Counting mapped keys for map org.At.tairCHRLENGTHS:
  - length(map) = 7
  - MAPCOUNTS["org.At.tairCHRLENGTHS"] = 7
  - count1 = 7 (0.001 s)
  - count2 = 7 (0 s)
  - count3 = 7 (0 s)
Counting mapped keys for map org.At.tairCHRLOC:
  - length(map) = 27416
  - MAPCOUNTS["org.At.tairCHRLOC"] = 27205
  - count1 = 27205 (0.091 s)
  - count2 = 27205 (0.056 s)
  - count3 = 27205 (0.268 s)
Counting mapped keys for map org.At.tairCHRLOCEND:
  - length(map) = 27416
  - MAPCOUNTS["org.At.tairCHRLOCEND"] = 27205
  - count1 = 27205 (0.086 s)
  - count2 = 27205 (0.055 s)
  - count3 = 27205 (0.253 s)
Counting mapped keys for map org.At.tairENZYME:
  - length(map) = 27416
  - MAPCOUNTS["org.At.tairENZYME"] = 2121
  - count1 = 2121 (0.008 s)
  - count2 = 2121 (0.008 s)
  - count3 = 2121 (0.175 s)
Counting mapped keys for map org.At.tairENZYME2TAIR:
  - length(map) = 723
  - MAPCOUNTS["org.At.tairENZYME2TAIR"] = 723
  - count1 = 723 (0.006 s)
  - count2 = 723 (0.008 s)
  - count3 = 723 (0.015 s)
Counting mapped keys for map org.At.tairGENENAME:
  - length(map) = 27416
  - MAPCOUNTS["org.At.tairGENENAME"] = 7804
  - count1 = 7804 (0.034 s)
  - count2 = 7804 (0.046 s)
  - count3 = 7804 (0.226 s)
Counting mapped keys for map org.At.tairGO:
  - length(map) = 27416
  - MAPCOUNTS["org.At.tairGO"] = 26863
  - count1 = 26863 (0.252 s)
  - count2 = 26863 (0.008 s)
  - count3 = 26863 (5.219 s)
Counting mapped keys for map org.At.tairGO2ALLTAIRS:
  - length(map) = 7436
  - MAPCOUNTS["org.At.tairGO2ALLTAIRS"] = 7436
  - count1 = 7436 (3.55 s)
  - count2 = 7436 (4.251 s)
  - count3 = 7436 (10.003 s)
Counting mapped keys for map org.At.tairGO2TAIR:
  - length(map) = 4890
  - MAPCOUNTS["org.At.tairGO2TAIR"] = 4890
  - count1 = 4890 (0.21 s)
  - count2 = 4890 (0.273 s)
  - count3 = 4890 (0.743 s)
Counting mapped keys for map org.At.tairPATH:
  - length(map) = 27416
  - MAPCOUNTS["org.At.tairPATH"] = 3450
  - count1 = 3450 (0.017 s)
  - count2 = 3450 (0.025 s)
  - count3 = 3450 (0.208 s)
Counting mapped keys for map org.At.tairPATH2TAIR:
  - length(map) = 123
  - MAPCOUNTS["org.At.tairPATH2TAIR"] = 123
  - count1 = 123 (0.009 s)
  - count2 = 123 (0.01 s)
  - count3 = 123 (0.018 s)
Counting mapped keys for map org.At.tairPMID:
  - length(map) = 27416
  - MAPCOUNTS["org.At.tairPMID"] = 22530
  - count1 = 22530 (0.251 s)
  - count2 = 22530 (0.127 s)
  - count3 = 22530 (0.396 s)
Counting mapped keys for map org.At.tairPMID2TAIR:
  - length(map) = 22060
  - MAPCOUNTS["org.At.tairPMID2TAIR"] = 22060
  - count1 = 22060 (0.271 s)
  - count2 = 22060 (0.287 s)
  - count3 = 22060 (0.597 s)
Counting mapped keys for map org.At.tairREFSEQ:
  - length(map) = 27416
  - MAPCOUNTS["org.At.tairREFSEQ"] = 27205
  - count1 = 27205 (0.166 s)
  - count2 = 27205 (0.08 s)
  - count3 = 27205 (0.356 s)
Counting mapped keys for map org.At.tairREFSEQ2TAIR:
  - length(map) = 70352
  - MAPCOUNTS["org.At.tairREFSEQ2TAIR"] = 70352
  - count1 = 70352 (0.268 s)
  - count2 = 70352 (0.288 s)
  - count3 = 70352 (1.061 s)
Counting mapped keys for map org.At.tairSYMBOL:
  - length(map) = 27416
  - MAPCOUNTS["org.At.tairSYMBOL"] = 11114
  - count1 = 11114 (0.05 s)
  - count2 = 11114 (0.039 s)
  - count3 = 11114 (0.325 s)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>