calculates the upper and lower elbow cut-off fold-values
a data.frame containing all of the fold values to calculate the elbow for.
a list containing the following:
up_limit — the upper (most positive) limit of the elbow curve
low_limit — the lower (most negative) limit of the elbow curve
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# read in the EcoliMutMA sample data from the package data(EcoliMutMA, package="ELBOW") csv_data <- EcoliMutMA # - OR - Read in a CSV file (uncomment - remove the #'s # - from the line below and replace 'filename' with # the CSV file's filename) # csv_data <- read.csv(filename) # set the number of initial and final condition replicates both to three init_count <- 3 final_count <- 3 # Parse the probes, intial conditions and final conditions # out of the CSV file. Please see: extract_working_sets # for more information. # # init_count should be the number of columns associated with # the initial conditions of the experiment. # final_count should be the number of columns associated with # the final conditions of the experiment. working_sets <- extract_working_sets(csv_data, init_count, final_count) probes <- working_sets[] initial_conditions <- working_sets[] final_conditions <- working_sets[] # Uncomment to output the plot to a PNG file (optional) # png(file="output_plot.png") my_data <- replicates_to_fold(probes, initial_conditions, final_conditions) # compute the elbow for the dataset limits <- do_elbow(data.frame(my_data$fold))