taxonomizr (version 0.2.2)

getTaxonomy: Get taxonomic ranks for a taxa

Description

Take NCBI taxa IDs and get the corresponding taxa ranks from name and node data.tables

Usage

getTaxonomy(ids, taxaNodes, taxaNames, desiredTaxa = c("superkingdom",
  "phylum", "class", "order", "family", "genus", "species"), mc.cores = 1,
  debug = FALSE)

Arguments

ids

a vector of ids to find taxonomy for

taxaNodes

a nodes data.table from read.nodes

taxaNames

a names data.table from read.names

desiredTaxa

a vector of strings giving the desired taxa levels

mc.cores

the number of cores to use when processing

debug

if TRUE output node and name vectors with dput for each id (probably useful only for development)

Value

a matrix of taxonomic strings with a row for each id and a column for each desiredTaxa rank

See Also

read.nodes, read.names

Examples

# NOT RUN {
namesText<-c(
  "1\t|\tall\t|\t\t|\tsynonym\t|",
  "1\t|\troot\t|\t\t|\tscientific name\t|",
  "2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tMonera\t|\tMonera <Bacteria>\t|\tin-part\t|",
  "2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|",
  "9606\t|\tHomo sapiens\t|\t\t|\tscientific name",
  "9605\t|\tHomo\t|\t\t|\tscientific name",
  "207598\t|\tHomininae\t|\t\t|\tscientific name",
  "9604\t|\tHominidae\t|\t\t|\tscientific name",
  "314295\t|\tHominoidea\t|\t\t|\tscientific name",
  "9526\t|\tCatarrhini\t|\t\t|\tscientific name",
  "314293\t|\tSimiiformes\t|\t\t|\tscientific name",
  "376913\t|\tHaplorrhini\t|\t\t|\tscientific name",
  "9443\t|\tPrimates\t|\t\t|\tscientific name",
  "314146\t|\tEuarchontoglires\t|\t\t|\tscientific name",
  "1437010\t|\tBoreoeutheria\t|\t\t|\tscientific name",
  "9347\t|\tEutheria\t|\t\t|\tscientific name",
  "32525\t|\tTheria\t|\t\t|\tscientific name",
  "40674\t|\tMammalia\t|\t\t|\tscientific name",
  "32524\t|\tAmniota\t|\t\t|\tscientific name",
  "32523\t|\tTetrapoda\t|\t\t|\tscientific name",
  "1338369\t|\tDipnotetrapodomorpha\t|\t\t|\tscientific name",
  "8287\t|\tSarcopterygii\t|\t\t|\tscientific name",
  "117571\t|\tEuteleostomi\t|\t\t|\tscientific name",
  "117570\t|\tTeleostomi\t|\t\t|\tscientific name",
  "7776\t|\tGnathostomata\t|\t\t|\tscientific name",
  "7742\t|\tVertebrata\t|\t\t|\tscientific name",
  "89593\t|\tCraniata\t|\t\t|\tscientific name",
  "7711\t|\tChordata\t|\t\t|\tscientific name",
  "33511\t|\tDeuterostomia\t|\t\t|\tscientific name",
  "33213\t|\tBilateria\t|\t\t|\tscientific name",
  "6072\t|\tEumetazoa\t|\t\t|\tscientific name",
  "33208\t|\tMetazoa\t|\t\t|\tscientific name",
  "33154\t|\tOpisthokonta\t|\t\t|\tscientific name",
  "2759\t|\tEukaryota\t|\t\t|\tscientific name",
  "131567\t|\tcellular organisms\t|\t\t|\tscientific name"
)
taxaNames<-read.names(textConnection(namesText))
nodesText<-c(
 "1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
  "2\t|\t131567\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|",
  "6\t|\t335928\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|",
  "7\t|\t6\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
  "9\t|\t32199\t|\tspecies\t|\tBA\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|",
  "9606\t|\t9605\t|\tspecies", "9605\t|\t207598\t|\tgenus", "207598\t|\t9604\t|\tsubfamily",
  "9604\t|\t314295\t|\tfamily", "314295\t|\t9526\t|\tsuperfamily",
  "9526\t|\t314293\t|\tparvorder", "314293\t|\t376913\t|\tinfraorder",
  "376913\t|\t9443\t|\tsuborder", "9443\t|\t314146\t|\torder",
  "314146\t|\t1437010\t|\tsuperorder", "1437010\t|\t9347\t|\tno rank",
  "9347\t|\t32525\t|\tno rank", "32525\t|\t40674\t|\tno rank",
  "40674\t|\t32524\t|\tclass", "32524\t|\t32523\t|\tno rank", "32523\t|\t1338369\t|\tno rank",
  "1338369\t|\t8287\t|\tno rank", "8287\t|\t117571\t|\tno rank",
  "117571\t|\t117570\t|\tno rank", "117570\t|\t7776\t|\tno rank",
  "7776\t|\t7742\t|\tno rank", "7742\t|\t89593\t|\tno rank", "89593\t|\t7711\t|\tsubphylum",
  "7711\t|\t33511\t|\tphylum", "33511\t|\t33213\t|\tno rank", "33213\t|\t6072\t|\tno rank",
  "6072\t|\t33208\t|\tno rank", "33208\t|\t33154\t|\tkingdom",
  "33154\t|\t2759\t|\tno rank", "2759\t|\t131567\t|\tsuperkingdom",
  "131567\t|\t1\t|\tno rank"
)
taxaNodes<-read.nodes(textConnection(nodesText))
getTaxonomy(c(9606,9605),taxaNodes,taxaNames,mc.cores=1)
# }