Calculate and Summarize Distribution of Susceptibilities by Gene

Calculate the distribution of susceptibilities by gene.

Usage

summarize_gene(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

a hagis.gene.summary object.

An object of class hagis.gene.summary is a
data.table::data.table() containing the following components columns

gene: the gene
N_virulent_isolates: the total number virulent isolates for a given gene in the gene column
percent_pathogenic: the frequency with which a gene is pathogenic

Examples

if (FALSE) { # interactive()
# Using the built-in data set, `P_sojae_survey`
data(P_sojae_survey)

P_sojae_survey

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