Barrick Lab :: ProtocolGrofit

---+ Calculating Growth Rates with Grofit

The following are instructions for calculating growth rates using Grofit, an R package that is no longer supported by the current version of R.

---++ Converting your file with OD data to the proper format
 What is most critical is the format and file type of the input data file containing the OD600 values. Most plate readers produce an Excel worksheet with the data results. With such a file, the first thing that must be done is to convert it to a comma delimited file. This is simply done by using "save as" in Excel and selecting *.csv as the file format. Your file should look similar to the one provided as example here: 
   * [[%ATTACHURL%/yourdatafile.csv][yourdatafile.csv]]: Example spreadsheet of your OD600 data file

---++ Create a "times only" csv file
 Grofit needs an additional file that will only have the times (e.g., 10, 20, 30 mins ...) for every time point measurement. An example of this file is given here: 
   * [[%ATTACHURL%/timesonlyworksheet.csv][timesonlyworksheet.csv]]: Times only worksheet for Grofit
It is critical that the number of time points in this file, match the number of OD readings on your data file.

---++ Calculating Growth Rates using Grofit R package
 The following is a short script (by Julie Perreau) on "R studio" that performs the downloading, installing, running and printing out results. You execute each line in the script by pressing Ctrl+Enter. For each one, you must check no errors are given. You can use the example timesonlyworksheet.csv and yourdatafile.csv files provided above as a test.
<pre>
<code>
setwd("C:/.../R_GrowthData") *#sets the working directory to the folder (here named R_GrowthData) you'll be working on your computer* <br /> install.packages(c("grofit", "tidyr", "reshape2"))<br /> library(grofit)<br /> library(tidyr)<br /> library(reshape2)<br /> <br /> growthdata &lt;- read.csv("yourdatafile.csv",sep=",", header=TRUE, check.names = FALSE) &lt;br/&gt; timedata &lt;- read.csv("timesonlyworksheet.csv", sep=",", header=TRUE, check.names = FALSE) &lt;br/&gt; gro &lt;- grofit(timedata, growthdata) *#runs grofit &lt;br/&gt;* <br /> summary_table&lt;-summary.gcFit(gro$gcFit) *#makes a summary table* &lt;br/&gt; write.csv(summary_table,"FinalTable.csv") *#makes a csv file of the summary table*
</code>
</pre>

---+++ Accepting/declining model fits:
 Once Grofit is run, you will be prompted to answer yes (y) or no (n) to accept or decline the model fits generated for each individual well. Most likely, all you need to do is say yes to *all* of them, unless there is some obvious model fit mistake which would make some sample unreliable. It is normal for Grofit to be unable to fit the curves to one of the 4 models tried, thus the ERROR sometimes given is not going to affect the final outcome, it just means it couldn't use one of the models to determine the best fit. <br /> <img width="880" alt="Satisfied.JPG" src="%ATTACHURLPATH%/Satisfied.JPG" height="402" />

---+++ Reading summary table results:

The table summary file produced by Grofit will give you all the parameter values (mu=GrowthRates, lambda=LagPhaseTime and A=MaxAbsorbance) generated from the best model fits. Grofit uses 4 possible models; see documentation for more information.

---++ References

   1 https://www.jstatsoft.org/article/view/v033i07
   1 https://cran.r-project.org/web/packages/grofit/index.html

Attachments

Topic attachments
I	Attachment	History	Action	Size	Date	Who	Comment
csv	timesonlyworksheet.csv	r1	manage	58.5 K	2021-11-03 - 21:46	IsaacGifford	Times only worksheet for Grofit
csv	yourdatafile.csv	r1	manage	159.8 K	2021-11-03 - 21:46	IsaacGifford	Example spreadsheet of your OD600 data file

Barrick Lab > ProtocolList > ProtocolsGrowthRates > ProtocolGrofit

Contributors to this topic

IsaacGifford

Topic revision: r1 - 2021-11-03 - 21:46:59 - Main.IsaacGifford