estimateGeneAge {PhyloProfile} | R Documentation |
Calculate the phylogenetic gene age from the phylogenetic profiles
estimateGeneAge(processedProfileData, taxaCount, rankName, refTaxon, var1CO, var2CO, percentCO)
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) |
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 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 )