Species Mapper object and/or list of valid taxonomy Ids

Description

A data frame containing a mapping between NCBI Taxonomy IDs and species OR a list of valid taxomony IDs (pre-subsetted and cleaned up from that same data.frame).

The reason why is because sometimes we need the entire frame, but other times we only need the list of integers, (which is much smaller and loads much more quickly)

The specData object is an even more complex data.frame that returns genus and species separately.

Usage

  data(speciesMap)
  data(validTaxIds)

Format

A data frame with 1416382 observations on the following 2 variables.

taxon

a numeric vector

species

a character vector

Author(s)

Marc Carlson

Examples

data(speciesMap)
sapply(speciesMap, class)   #       taxon     species 
                            #    "integer" "character" 
subset(speciesMap, species=="Homo sapiens")$taxon # [1] 9606

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/speciesMap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: speciesMap
> ### Title: Species Mapper object and/or list of valid taxonomy Ids
> ### Aliases: speciesMap validTaxIds specData
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(speciesMap)
> sapply(speciesMap, class)   #       taxon     species 
      taxon     species 
"character" "character" 
>                             #    "integer" "character" 
> subset(speciesMap, species=="Homo sapiens")$taxon # [1] 9606
[1] "9606"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>