estimateGeneAge {PhyloProfile} | R Documentation |
Calculate the phylogenetic gene age from the phylogenetic profiles
estimateGeneAge(processedProfileData, rankName, refTaxon, var1CO, var2CO, percentCO)
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 |
var2CO |
cutoff for var2 |
percentCO |
cutoff for percentage of species present in each supertaxon |
A dataframe contains estimated gene ages for the seed proteins.
Vinh Tran tran@bio.uni-frankfurt.de
parseInfoProfile
for creating a full processed
profile dataframe; getNameList
and
getTaxonomyMatrix
for getting taxonomy info,
fullProcessedProfile
for a demo input dataframe
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 )