calculate_complexities: Calculate Distribution of Complexities by Sample

In hagis: Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity

Calculate Distribution of Complexities by Sample

Description

Calculate the distribution of susceptibilities by sample id.

Usage

calculate_complexities(x, cutoff, control, sample, gene, perc_susc)

Arguments

x	a data.frame containing the data.
cutoff	value for percent susceptible cutoff. Numeric.
control	value used to denote the susceptible control in the gene column. Character.
sample	column providing the unique identification for each sample being tested. Character.
gene	column providing the gene(s) being tested. Character.
perc_susc	column providing the percent susceptible reactions. Character.

Value

calculate_complexities returns an object of class hagis.complexities.

An object of class hagis.complexities is a list containing the following components

grouped_complexities

a data.table::data.table() object of grouped complexities

individual_complexities

a data.table::data.table() object of individual complexities

Examples

# Using the built-in data set, `P_sojae_survey`
data(P_sojae_survey)

P_sojae_survey

# calculate susceptibilities with a 60 % cutoff value
complexities <- calculate_complexities(x = P_sojae_survey,
                                       cutoff = 60,
                                       control = "susceptible",
                                       sample = "Isolate",
                                       gene = "Rps",
                                       perc_susc = "perc.susc")
complexities

summary(complexities)

hagis documentation built on Sept. 8, 2023, 5:20 p.m.