estimate_gene_age: Calculate the phylogenetic gene age from profiles

In trvinh/test: PhyloProfile

Description

Calculate the phylogenetic gene age from profiles

Usage

estimate_gene_age(processed_profile_data, rank_name, ref_taxon,
    var1_cutoff, var2_cutoff, percent_cutoff)

Arguments

processed_profile_data	dataframe contains the full processed phylogenetic profiles
rank_name	taxonomy rank (e.g. "species", "genus", "family")
ref_taxon	reference taxon (e.g. "Homo sapiens", "Homo", "Hominidae")
var1_cutoff	cutoff for var1
var2_cutoff	cutoff for var2
percent_cutoff	cutoff for percentage of species present in each supertaxon

Value

A dataframe contains estimated gene ages

Author(s)

Vinh Tran [e-mail]

See Also

parse_info_profile for creating a full processed profile dataframe; get_name_list and get_taxonomy_matrix for getting taxonomy info, full_processed_profile for a demo input dataframe

Examples

data("full_processed_profile", package="phyloprofile")
rank_name <- "class"
ref_taxon <- "Mammalia"
processed_profile_data <- full_processed_profile
var1_cutoff <- c(0, 1)
var2_cutoff <- c(0, 1)
percent_cutoff <- c(0, 1)
estimate_gene_age(
    processed_profile_data,
    rank_name,
    ref_taxon,
    var1_cutoff, var2_cutoff, percent_cutoff
)

trvinh/test documentation built on May 9, 2019, 2:26 a.m.