estimateGeneAge: Calculate the phylogenetic gene age from the phylogenetic...

In BIONF/PhyloProfile: PhyloProfile

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, taxDB = NULL)

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)
taxDB	Path to the taxonomy DB files

Value

A dataframe contains estimated gene ages for the seed proteins.

Author(s)

Vinh Tran [e-mail]

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, 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
)

BIONF/PhyloProfile documentation built on April 14, 2024, 10:39 p.m.