Last data update: 2014.03.03

 R: Check the SQL data contained in an SQLite-based annotation...
AnnDbPkg-checkerR Documentation

Check the SQL data contained in an SQLite-based annotation package

Description

Check the SQL data contained in an SQLite-based annotation package.

Usage

  checkMAPCOUNTS(pkgname)

Arguments

pkgname

The name of the SQLite-based annotation package to check.

Author(s)

H. Pages

See Also

AnnDbPkg-maker

Examples

  checkMAPCOUNTS("org.Sc.sgd.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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(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/AnnotationDbi/AnnDbPkg-checker.Rd_%03d_medium.png", width=480, height=480)
> ### Name: AnnDbPkg-checker
> ### Title: Check the SQL data contained in an SQLite-based annotation
> ###   package
> ### Aliases: AnnDbPkg-checker checkMAPCOUNTS
> ### Keywords: utilities
> 
> ### ** Examples
> 
>   checkMAPCOUNTS("org.Sc.sgd.db")
Loading required package: org.Sc.sgd.db

Counting mapped keys for map org.Sc.sgdALIAS:
  - length(map) = 8058
  - MAPCOUNTS["org.Sc.sgdALIAS"] = 4462
  - count1 = 4462 (0.022 s)
  - count2 = 4462 (0.016 s)
  - count3 = 4462 (0.076 s)
Counting mapped keys for map org.Sc.sgdCHR:
  - length(map) = 8058
  - MAPCOUNTS["org.Sc.sgdCHR"] = 8058
  - count1 = 8058 (0.036 s)
  - count2 = 8058 (0.019 s)
  - count3 = 8058 (0.081 s)
Counting mapped keys for map org.Sc.sgdCHRLENGTHS:
  - length(map) = 17
  - MAPCOUNTS["org.Sc.sgdCHRLENGTHS"] = 17
  - count1 = 17 (0.001 s)
  - count2 = 17 (0 s)
  - count3 = 17 (0 s)
Counting mapped keys for map org.Sc.sgdCHRLOC:
  - length(map) = 8058
  - MAPCOUNTS["org.Sc.sgdCHRLOC"] = 7993
  - count1 = 7993 (0.036 s)
  - count2 = 7993 (0.019 s)
  - count3 = 7993 (0.053 s)
Counting mapped keys for map org.Sc.sgdCHRLOCEND:
  - length(map) = 8058
  - MAPCOUNTS["org.Sc.sgdCHRLOCEND"] = 7993
  - count1 = 7993 (0.02 s)
  - count2 = 7993 (0.011 s)
  - count3 = 7993 (0.051 s)
Counting mapped keys for map org.Sc.sgdCOMMON2ORF:
  - length(map) = 12232
  - MAPCOUNTS["org.Sc.sgdCOMMON2ORF"] = 12232
  - count1 = 12232 (0.022 s)
  - count2 = 12232 (0.029 s)
  - count3 = 12232 (0.106 s)
Counting mapped keys for map org.Sc.sgdDESCRIPTION:
  - length(map) = 8058
  - MAPCOUNTS["org.Sc.sgdDESCRIPTION"] = 8052
  - count1 = 8052 (0.018 s)
  - count2 = 8052 (0.012 s)
  - count3 = 8052 (0.055 s)
Counting mapped keys for map org.Sc.sgdENSEMBL:
  - length(map) = 8058
  - MAPCOUNTS["org.Sc.sgdENSEMBL"] = 5876
  - count1 = 5876 (0.012 s)
  - count2 = 5876 (0.012 s)
  - count3 = 5876 (0.073 s)
Counting mapped keys for map org.Sc.sgdENSEMBL2ORF:
  - length(map) = 5883
  - MAPCOUNTS["org.Sc.sgdENSEMBL2ORF"] = 5883
  - count1 = 5883 (0.02 s)
  - count2 = 5883 (0.022 s)
  - count3 = 5883 (0.075 s)
Counting mapped keys for map org.Sc.sgdENSEMBLPROT:
  - length(map) = 8058
  - MAPCOUNTS["org.Sc.sgdENSEMBLPROT"] = 5876
  - count1 = 5876 (0.02 s)
  - count2 = 5876 (0.014 s)
  - count3 = 5876 (0.071 s)
Counting mapped keys for map org.Sc.sgdENSEMBLPROT2ORF:
  - length(map) = 5883
  - MAPCOUNTS["org.Sc.sgdENSEMBLPROT2ORF"] = 5883
  - count1 = 5883 (0.02 s)
  - count2 = 5883 (0.023 s)
  - count3 = 5883 (0.076 s)
Counting mapped keys for map org.Sc.sgdENSEMBLTRANS:
  - length(map) = 8058
  - MAPCOUNTS["org.Sc.sgdENSEMBLTRANS"] = 5876
  - count1 = 5876 (0.02 s)
  - count2 = 5876 (0.014 s)
  - count3 = 5876 (0.077 s)
Counting mapped keys for map org.Sc.sgdENSEMBLTRANS2ORF:
  - length(map) = 5883
  - MAPCOUNTS["org.Sc.sgdENSEMBLTRANS2ORF"] = 5883
  - count1 = 5883 (0.02 s)
  - count2 = 5883 (0.022 s)
  - count3 = 5883 (0.075 s)
Counting mapped keys for map org.Sc.sgdENTREZID:
  - length(map) = 8058
  - MAPCOUNTS["org.Sc.sgdENTREZID"] = 6350
  - count1 = 6350 (0.02 s)
  - count2 = 6350 (0.014 s)
  - count3 = 6350 (0.043 s)
Counting mapped keys for map org.Sc.sgdENZYME:
  - length(map) = 8058
  - MAPCOUNTS["org.Sc.sgdENZYME"] = 981
  - count1 = 981 (0.004 s)
  - count2 = 981 (0.007 s)
  - count3 = 981 (0.051 s)
Counting mapped keys for map org.Sc.sgdENZYME2ORF:
  - length(map) = 561
  - MAPCOUNTS["org.Sc.sgdENZYME2ORF"] = 561
  - count1 = 561 (0.003 s)
  - count2 = 561 (0.005 s)
  - count3 = 561 (0.013 s)
Counting mapped keys for map org.Sc.sgdGENENAME:
  - length(map) = 8058
  - MAPCOUNTS["org.Sc.sgdGENENAME"] = 5427
  - count1 = 5427 (0.019 s)
  - count2 = 5427 (0.012 s)
  - count3 = 5427 (0.07 s)
Counting mapped keys for map org.Sc.sgdGO:
  - length(map) = 8058
  - MAPCOUNTS["org.Sc.sgdGO"] = 6381
  - count1 = 6381 (0.114 s)
  - count2 = 6381 (0.007 s)
  - count3 = 6381 (1.744 s)
Counting mapped keys for map org.Sc.sgdGO2ALLORFS:
  - length(map) = 8451
  - MAPCOUNTS["org.Sc.sgdGO2ALLORFS"] = 8451
  - count1 = 8451 (1.161 s)
  - count2 = 8451 (1.432 s)
  - count3 = 8451 (3.166 s)
Counting mapped keys for map org.Sc.sgdGO2ORF:
  - length(map) = 5543
  - MAPCOUNTS["org.Sc.sgdGO2ORF"] = 5543
  - count1 = 5543 (0.059 s)
  - count2 = 5543 (0.083 s)
  - count3 = 5543 (0.163 s)
Counting mapped keys for map org.Sc.sgdINTERPRO:
  - length(map) = 8058
  - MAPCOUNTS["org.Sc.sgdINTERPRO"] = 301
  - count1 = 301 (0.004 s)
  - count2 = 301 (0.004 s)
  - count3 = 301 (0.058 s)
Counting mapped keys for map org.Sc.sgdPATH:
  - length(map) = 8058
  - MAPCOUNTS["org.Sc.sgdPATH"] = 2024
  - count1 = 2024 (0.011 s)
  - count2 = 2024 (0.012 s)
  - count3 = 2024 (0.067 s)
Counting mapped keys for map org.Sc.sgdPATH2ORF:
  - length(map) = 99
  - MAPCOUNTS["org.Sc.sgdPATH2ORF"] = 99
  - count1 = 99 (0.006 s)
  - count2 = 99 (0.006 s)
  - count3 = 99 (0.013 s)
Counting mapped keys for map org.Sc.sgdPMID:
  - length(map) = 8058
  - MAPCOUNTS["org.Sc.sgdPMID"] = 8046
  - count1 = 8046 (0.723 s)
  - count2 = 8046 (0.312 s)
  - count3 = 8046 (0.666 s)
Counting mapped keys for map org.Sc.sgdPMID2ORF:
  - length(map) = 69250
  - MAPCOUNTS["org.Sc.sgdPMID2ORF"] = 69250
  - count1 = 69250 (0.496 s)
  - count2 = 69250 (0.532 s)
  - count3 = 69250 (1.361 s)
Counting mapped keys for map org.Sc.sgdREFSEQ:
  - length(map) = 8058
  - MAPCOUNTS["org.Sc.sgdREFSEQ"] = 6030
  - count1 = 6030 (0.014 s)
  - count2 = 6030 (0.013 s)
  - count3 = 6030 (0.075 s)
Counting mapped keys for map org.Sc.sgdREJECTORF:
  - length(map) = 496
  - MAPCOUNTS["org.Sc.sgdREJECTORF"] = 496
  - count1 = 496 (0 s)
Counting mapped keys for map org.Sc.sgdSMART:
  - length(map) = 8058
  - MAPCOUNTS["org.Sc.sgdSMART"] = 1658
  - count1 = 1658 (0.005 s)
  - count2 = 1658 (0.005 s)
  - count3 = 1658 (0.051 s)
Counting mapped keys for map org.Sc.sgdUNIPROT:
  - length(map) = 8058
  - MAPCOUNTS["org.Sc.sgdUNIPROT"] = 5907
  - count1 = 5907 (0.012 s)
  - count2 = 5907 (0.009 s)
  - count3 = 5907 (0.065 s)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO