R/create_binary_matrix.R
create_binary_matrix.Rd
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)
a data.frame
containing the data.
value for percent susceptible cutoff. Numeric
.
value used to denote the susceptible control in the gene
column. Character
.
column providing the unique identification for each sample
being tested. Character
.
column providing the gene(s) being tested. Character
.
column providing the percent susceptible reactions.
Character
.
create_binary_matrix
returns a binary matrix of pathotype data as
a matrix object
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
}