getCoreGene: Identify core genes for a list of selected taxa

In PhyloProfile: PhyloProfile

Description

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).

Usage

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

Arguments

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.

Value

A list of identified core genes.

Author(s)

Vinh Tran [e-mail]

See Also

parseInfoProfile for creating a full processed profile dataframe

Examples

data("fullProcessedProfile", package="PhyloProfile")
rankName <- "class"
refTaxon <- "Mammalia"
taxaCore <- c("Mammalia", "Saccharomycetes", "Insecta")
profileDt <- fullProcessedProfile
taxonIDs <- levels(as.factor(fullProcessedProfile$ncbiID))
sortedInputTaxa <- sortInputTaxa(
    taxonIDs, rankName, refTaxon, NULL
)
taxaCount <- plyr::count(sortedInputTaxa, "supertaxon")
var1Cutoff <- c(0.75, 1.0)
var2Cutoff <- c(0.75, 1.0)
percentCutoff <- c(0.0, 1.0)
coreCoverage <- 100
getCoreGene(
    rankName,
    taxaCore,
    profileDt,
    taxaCount,
    var1Cutoff, var2Cutoff,
    percentCutoff, coreCoverage
)

PhyloProfile documentation built on March 27, 2021, 6:01 p.m.