parse_info_profile: Parsing info for phylogenetic profiles

In trvinh/test: PhyloProfile

Description

Creating main dataframe for the input phylogenetic profiles with the selected input taxonomy level (e.g. strain, species) and reference taxon. The output contains the number of paralogs, percentage of species presence in each supertaxon, and the max/min/mean/median of VAR1 and VAR2.

Usage

parse_info_profile( input_df, sorted_input_taxa, var1_aggregate_by, 
    var2_aggregate_by)

Arguments

input_df	input profiles in long format
sorted_input_taxa	sorted taxonomy data for the input taxa (check sort_input_taxa())
var1_aggregate_by	aggregate method for VAR1 (min, max, mean or median)
var2_aggregate_by	aggregate method for VAR2 (min, max, mean or median)

Value

Dataframe contains all info for input profiles (a full processed profile)

Author(s)

Vinh Tran [e-mail]

See Also

create_long_matrix, sort_input_taxa, calc_pres_spec, main_long_raw

Examples

data("main_long_raw", package="phyloprofile")
input_df <- main_long_raw
taxon_IDs <- get_input_taxa_id(input_df)
taxon_names <- get_input_taxa_name("class", taxon_IDs)
sorted_input_taxa <- sort_input_taxa(
    taxon_IDs, taxon_names, "class", "Mammalia", NULL
)
var1_aggregate_by <- "max"
var2_aggregate_by <- "mean"
parse_info_profile(
    input_df, sorted_input_taxa, var1_aggregate_by, var2_aggregate_by
)

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