getCoreGeneCr: Identify core genes for a list of selected taxa
In trvinh/PhyloProfileCorona: PhyloProfileCorona

Description Usage Arguments Value Author(s)

View source: R/identifyCoreGene.R

Identify core genes for a list of selected (super)taxa. The identified core genes must be present in at least a certain proportion of species in each selected (super)taxon (identified via percentCutoff) and that criteria must be fullfilled for a certain percentage of selected taxa or all of them (determined via coreCoverage).

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getCoreGeneCr(rankName, taxaCore = c("none"), profileDt, taxaCount,
    var1Cutoff = c(0, 1), var2Cutoff = c(0, 1), percentCutoff = c(0, 1),
    coreCoverage = 100)

`rankName`	working taxonomy rank (e.g. "species", "genus", "family")
`taxaCore`	list of selected taxon names
`profileDt`	dataframe contains the full processed phylogenetic profiles (see ?fullProcessedProfile or ?parseInfoProfile)
`taxaCount`	dataframe counting present taxa in each supertaxon
`var1Cutoff`	cutoff for var1. Default = c(0, 1).
`var2Cutoff`	cutoff for var2. Default = c(0, 1).
`percentCutoff`	cutoff for percentage of species present in each supertaxon. Default = c(0, 1).
`coreCoverage`	the least percentage of selected taxa should be considered. Default = 1.