taxFun: Run taxFun

In trvinh/taxFun: taxFun

Run taxFun

Description

Run taxFun

Usage

taxFun(fnName, inputTaxaFile, rank, ranks, refspec, supertaxon, 
outgroup, outputFile)

Arguments

fnName	Function name, either "id2name", "name2id", "getRank", "getRanks", "sortTaxonomyMatrix", "createTree", "createTreeSlow", "getRepresentative", "getClade", "getLCA" or "getAllTaxonomyRanks"
inputTaxaFile	Location of input taxa file (taxon names or/and ids)
rank	A selected taonomy rank (REQUIRED for some functions)
ranks	List of taxonomy ranks of interest (OPTIONAL)
refspec	Reference species (REQUIRED for some functions)
supertaxon	Supertaxon name or ID (REQUIRED for some functions)
outgroup	Output species used for rooting the tree (OPTIONAL for tree functions)
outputFile	Location of output file. If not given, it will be saved as <inputFile.out>

Value

Output file

Examples

inputTaxonIDs <- system.file(
    "extdata", "ids.txt", package = "taxFun", mustWork = TRUE
)
inputTaxonNames <- system.file(
    "extdata", "names.txt", package = "taxFun", mustWork = TRUE
)
taxFun("id2name", inputTaxonIDs)
taxFun("getRank", inputTaxonNames)
taxFun("getRanks", inputTaxonNames, ranks = c("class", "phylum"))
taxFun("createTree", inputTaxonNames, outgroup = 9606)
taxFun("sortTaxonomyMatrix", inputTaxonIDs, refspec = "Homo sapiens")
taxFun("getRepresentative", inputTaxonIDs, rank = "phylum")
taxFun("getClade", inputTaxonIDs, supertaxon = "metazoa")
taxFun("getLCA", inputTaxonNames)

trvinh/taxFun documentation built on July 3, 2023, 8:55 p.m.