Instructions for how to analyze fluctuation test data using the command line. Please see this page for information regarding how to conduct a fluctuation analysis.

Installing rSalvador

Before the Rscript can be used, rSalvador needs to be installed locally. Unfortuantely this can't be done using normal R commands (in other words install.packages("rsalvador") doesn't work) rSalvador should be cloned from github here

  1. git clone https://github.com/eeeeeric/rSalvador.git
  2. cd rSalvador
  3. R CMD cherck rsalvador
  4. R CMD INSTALL rsalvador

Installing Barricklab general github

If you havn't already installed the general Barricklab project from github, do so. It is assumed that you install it in ~/src but it can be installed anywhere and adjusted accordingly. Github project is located here.

  1. git clone https://github.com/barricklab/barricklab.git

Executing the fluxxer.R script

Things you need

  1. A .csv file contianing count data.
  2. Knowledge of the following as it relates to the non-selctive plates (if they differ from the default values).
    1. Original culture volume
    2. Dilution factor
    3. Volume plated
  3. Desired prefix for output files.

Input.csv file

The script is designed to read in all count data from a .csv file formated as follows.

  • Columns: Each column represents a single sample and will contain both selective and non-selective counts. Sample order determines graph output.
  • Row 1: Name of sample.
    • This will be displayed verbatim on the resulting graph.
  • Row 2-n: Selective plate counts.
    • Single plate per row, as many rows as plates were counted.
  • Row n+1: Non_Selective
    • Text must appear exactly as typed above (capital N and S with single underscore between).
    • Can appear on different rows for different samples if different numbers of selective plates were counted.
  • Row n+2-last: Non_Selective plate counts.
    • Single plate per row, as many rows as plates were counted.
    • Rows should be actual counts, without any calculation of what the original culture concentration was.

Execution

-- Main.DanielDeatherage - 07 Dec 2017

 Barrick Lab  >  ProtocolsFluctuationTests  >  FluctuationAnalysis

Topic revision: r3 - 14 Dec 2017 - 22:10:41 - Main.DanielDeatherage
 
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