analyze_elbow {ELBOW} | R Documentation

## extracts all elbow statistics and plots and elbow curve.

### Description

Analyzes:

- the Elbow cut-offs

- the Elbow curve variance

- the upper and lower error Elbow curves

- \logχ^2 p-value for the Elbow curve model

### Usage

      analyze_elbow(probes, initial_conditions,
        final_conditions, gtitle = "")

### Arguments

`probes` | the data set of probes (as a data.frame).
`initial_conditions` | a 2D data.fram containing all of the replicate gene expression values corresponding to the experiment's initial conditions.
`final_conditions` | a 2D data.fram containing all of the replicate gene expression values corresponding to the experiment's final conditions.
`gtitle` | the title to display for the graph.

### Details

Then plots the data to a curve - AND - prints the statistics to both the terminal and the plot canvas.

### Value

a list of all significant probes

### 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")

    		# Analyze the elbow curve.
    		sig <- analyze_elbow(probes, initial_conditions, final_conditions)

    		# write the significant probes to 'signprobes.csv'
    		write.table(sig,file="signprobes.csv",sep=",",row.names=FALSE)

[Package ELBOW version 1.16.0 Index]