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, rankName, refTaxon,
    var1CO, var2CO, percentCO)

Arguments

processedProfileData

dataframe contains the full processed phylogenetic profiles (see ?fullProcessedProfile or ?parseInfoProfile)

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
var1Cutoff <- c(0, 1)
var2Cutoff <- c(0, 1)
percentCutoff <- c(0, 1)
estimateGeneAge(
    processedProfileData,
    rankName,
    refTaxon,
    var1Cutoff, var2Cutoff, percentCutoff
)
[Package PhyloProfile version 1.2.8 Index]