do_elbow {ELBOW} | R Documentation

## calculates the upper and lower elbow cut-off fold-values

### Description

calculates the upper and lower elbow cut-off fold-values

### Usage

      do_elbow(fold_values)

### Arguments

`fold_values` | a data.frame containing all of the fold values to calculate the elbow for.

### Value

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

### Examples

    # 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[[1]]
    		initial_conditions <- working_sets[[2]]
    		final_conditions <- working_sets[[3]]

    		# 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))

[Package ELBOW version 1.18.1 Index]