getCoreGene {PhyloProfile} | R Documentation

## Identify core genes for a list of selected taxa

### 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 tran@bio.uni-frankfurt.de

### 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
    )

[Package PhyloProfile version 1.4.11 Index]