loadTaxonomyDb: Return a data.frame that lists the known taxonomy IDs and...

In GenomeInfoDb: Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

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 organism).

Usage

  loadTaxonomyDb()

Value

A data frame with 1 row per genus/species designation and three columns. The 1st column is the taxonomy ID. The second columns is the genus and the third is the species name.

Author(s)

Marc Carlson

Examples

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

Example output

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, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
         tax_id        genus     species
2459835 2777733   Terminalia    coronata
2459836 2777734   Buchenavia pulcherrima
2459837 2777734   Buchenavia  reticulata
2459838 2777734   Terminalia pulcherrima
2459839 2777781   Rufibacter     sp. LB8
2459840 2777940 unclassified      Cercis
         tax_id      genus                   species
8835       5861 Plasmodium                    yoelii
8837       5862 Plasmodium            berghei yoelii
21319     31274 Plasmodium        yoelii nigeriensis
21320     31274 Plasmodium yoelii subsp. nigeriensis
68060     73239 Plasmodium      yoelii subsp. yoelii
68061     73239 Plasmodium             yoelii yoelii
286213   283801 Plasmodium           yoelii killicki
356727   352914 Plasmodium       yoelii yoelii 17XNL
356728   352914 Plasmodium  yoelii yoelii str. 17XNL
916764  1050261 Plasmodium                 yoelii YM
916765  1050262 Plasmodium                 yoelii 17
1176752 1323249 Plasmodium                yoelii 17X

GenomeInfoDb documentation built on April 9, 2021, 6 p.m.