estimateGeneAge {PhyloProfile} | R Documentation

## Calculate the phylogenetic gene age from the phylogenetic profiles

### Description

Calculate the phylogenetic gene age from the phylogenetic profiles

### Usage

    estimateGeneAge(processedProfileData, taxaCount, rankName, refTaxon,
        var1CO, var2CO, percentCO)

### Arguments

`processedProfileData` | dataframe contains the full processed phylogenetic profiles (see ?fullProcessedProfile or ?parseInfoProfile)
`taxaCount` | dataframe counting present taxa in each supertaxon
`rankName` | working taxonomy rank (e.g. "species", "genus", "family")
`refTaxon` | reference taxon name (e.g. "Homo sapiens", "Homo" or "Hominidae")
`var1CO` | cutoff for var1. Default: c(0, 1)
`var2CO` | cutoff for var2. Default: c(0, 1)
`percentCO` | cutoff for percentage of species present in each supertaxon. Default: c(0, 1)

### Value

A dataframe contains estimated gene ages for the seed proteins.

### Author(s)

Vinh Tran tran@bio.uni-frankfurt.de

### See Also

`parseInfoProfile` for creating a full processed profile dataframe; `getNameList` and `getTaxonomyMatrix` for getting taxonomy info, `fullProcessedProfile` for a demo input dataframe

### Examples

    data("fullProcessedProfile", package="PhyloProfile")
    rankName <- "class"
    refTaxon <- "Mammalia"
    processedProfileData <- fullProcessedProfile
    taxonIDs <- levels(as.factor(processedProfileData$ncbiID))
    sortedInputTaxa <- sortInputTaxa(
        taxonIDs, rankName, refTaxon, NULL
    )
    taxaCount <- plyr::count(sortedInputTaxa, "supertaxon")
    var1Cutoff <- c(0, 1)
    var2Cutoff <- c(0, 1)
    percentCutoff <- c(0, 1)
    estimateGeneAge(
        processedProfileData,
        taxaCount,
        rankName,
        refTaxon,
        var1Cutoff, var2Cutoff, percentCutoff
    )

[Package PhyloProfile version 1.4.11 Index]