Create Binary Data Matrix From Pathotype Data — create_binary

Creates a binary data matrix from pathotype data representing the pathotype of each isolate. This binary data matrix can be used to visualize beta-diversity of pathotypes using vegan and ape.

create_binary_matrix(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

create_binary_matrix returns a binary matrix of pathotype data as a matrix object

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
final_matrix <- create_binary_matrix(x = P_sojae_survey,
                                    cutoff = 60,
                                    control = "susceptible",
                                    sample = "Isolate",
                                    gene = "Rps",
                                    perc_susc = "perc.susc")
final_matrix
}