calculate_complexities {hagis}

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

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)