Returns a data.frame that lists the available species strings and their taxonomy Ids.

Description

NCBI maintains a collection of unique taxonomy Ids and pairs these with associated genus and species designations. This function returns the set of pre-processed values that we use to check that something is a valid Taxonomy ID (or species name)

Usage

  available.species()

Value

A data frame with 1 row per species designation and two columns. The 1st column is the taxonomy Id. The second columns is the species name.

Author(s)

Marc Carlson

Examples

  ## get the data
  spec <- available.species()
  tail(spec)
  ## which can then be searched etc.
  spec[grepl('yoelii',spec$species),]

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(GenomeInfoDb)
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: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GenomeInfoDb/availableSpecies.Rd_%03d_medium.png", width=480, height=480)
> ### Name: available.species
> ### Title: Returns a data.frame that lists the available species strings
> ###   and their taxonomy Ids.
> ### Aliases: available.species
> ### Keywords: manip
> 
> ### ** Examples
> 
>   ## get the data
>   spec <- available.species()
>   tail(spec)
          taxon                        species
1480762 1655516 unclassified Pelagibacteraceae
1480763 1655637                 'Lokiarchaeum'
1480764 1656058                   Calaphididae
1480765 1656058                   Calaphidinae
1480766 1656090              Neophyllaphidinae
1480767 1656091                     Tamaliinae
>   ## which can then be searched etc.
>   spec[grepl('yoelii',spec$species),]
          taxon                              species
9384       5861                    Plasmodium yoelii
9386       5862            Plasmodium berghei yoelii
24312     31274        Plasmodium yoelii nigeriensis
24313     31274 Plasmodium yoelii subsp. nigeriensis
75330     73239      Plasmodium yoelii subsp. yoelii
75331     73239             Plasmodium yoelii yoelii
307030   283801           Plasmodium yoelii killicki
384574   352914       Plasmodium yoelii yoelii 17XNL
384575   352914  Plasmodium yoelii yoelii str. 17XNL
967647  1050261                 Plasmodium yoelii YM
967648  1050262                 Plasmodium yoelii 17
1224921 1323249                Plasmodium yoelii 17X
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>