get_core_gene: Identify core genes for a list of selected taxa

In trvinh/test: PhyloProfile

Description

Identify core genes for a list of selected taxa

Usage

get_core_gene(rank_name, taxa_core, processed_profile_data,
    var1_cutoff, var2_cutoff, percent_cutoff, core_coverage)

Arguments

rank_name	taxonomy rank (e.g. "species", "genus", "family")
taxa_core	name list of selected taxa
processed_profile_data	dataframe contains the full processed phylogenetic profiles
var1_cutoff	cutoff for var1
var2_cutoff	cutoff for var2
percent_cutoff	cutoff for percentage of species present in each supertaxon
core_coverage	the least number of selected taxa should be considered

Value

A list of core genes

Author(s)

Vinh Tran [e-mail]

See Also

parse_info_profile for creating a full processed profile dataframe

Examples

data("full_processed_profile", package="phyloprofile")
rank_name <- "class"
taxa_core <- c("Mammalia", "Mucorales", "Alphaproteobacteria")
processed_profile_data <- full_processed_profile
var1_cutoff <- c(0.75, 1.0)
var2_cutoff <- c(0.75, 1.0)
percent_cutoff <- c(0.0, 1.0)
core_coverage <- 1
get_core_gene(
    rank_name,
    taxa_core,
    processed_profile_data,
    var1_cutoff, var2_cutoff,
    percent_cutoff, core_coverage
)

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