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README.md
mutationalAux.js
mutationalBias.js
mutationalCounter.js

README.md

mutant_calculator

This app is available on www.mutanalyst.com.
A full copy of the website, including third party tools (credits go to respective authors, vide infra), can be found in my dropbox, please note that the author (me) is not affiated with the third party tools. If used please cite:

Ferla MP. Mutanalyst, an online tool for assessing the mutational spectrum of epPCR libraries with poor sampling.
BMC Bioinformatics. 2016 Apr 4;17:152.

Which can be found:

Overview

This section details how the program works and its knowledge is not needed to use the program. It is intended as an overview in case a researcher wanted to alter it for a different purpose or copy a function from it.
Mutanalysis is composed of three HTML pages:

  • Mutational_bias_calculator
  • Mutation_counter
  • Variance_notes

Each page uses a cetral CSS file, mut.css, and two external style resources, Font-Awesome and the Source Sans Pro (Google fonts), two commonly used resources used in contemporary webpages.

The three html pages also use several external JavaScript (JS) resources:

  • JQuery, an essential library that greatly simplifies JS coding.
  • Tooltip JS (and Tether JS and Drop JS, and its style sheet), a library used to make tootips (notes on hover), which have several advantages over the inbuilt title attribute of html tags.
  • Google Charts, a JS library that allows charts to be plotted, part of the Google Developers tool kit.
  • Google Analytics, a JS widget that send asynchronously data to Google allowing the author to see what browsers are being used. At present, Mutanalyst is optimally viewed with Google Chrome on a Mac or Windows, but that may change in the future.

Additionally the page Mutational_counter.htm uses a specific JS file, mutationalCounter.js while Mutational_bias_calculator.htm uses two specific JS files:

  • mutationalBias.js, a script that handles the calculations and does not interact with the document or utilise any other script.
  • mutationalAux.js, a script that handles all the events of the buttons and other document interactions.

The key object in the mutationalBias.js calculations is called “mutball” (following after tarball etc., a personal coding preference which I have blogged about), which store all the variables and contains several keys that match the id of elements in the html document allowing mutationalAux.js to modify them without unnecessary coding. Its constructor is called mutagen. With a few exceptions (radio buttons, which do not call mutationalBias.js) it is recreated in case the user alters anything. The exception get the object via SessionStorage. The attributes can additionally be passed by URL query string. Some of the attributes are:

  • source: a string noting whence the object was called.
  • sequence: e.g. ATATCGG.
  • baseList: e.g. G286A T306C A687T T880C\nWT\nWT.
  • freqMean: mean frequency of number of mutations per sequence, a simple arithmetic average.
  • freqVar: variance of number of mutations per sequence.
  • freqList: array of the mutation counts (binned) of the rows of baselist.
  • freqΣ: sum of number of mutations per sequence sampled.
  • freqλ: Poisson distribution of number of mutations per sequence.
  • rawTable: 4x4 nested arrays containing the mutation spectrum observed.
  • mutTable: as above but normalised.
  • sumA, vsumT` etc. the number of As in the sequence.
  • A2T etc. number of incidents going from A to T. There are 16 of these. It is redundant with rawTable: but for html reasons it’s repeated.
  • size: gene size in kb.
  • TsOverTv and TsOverTv_error: transitions over transversions and its error. The keys with errors are as follows (they codes are: W=weak AT, S=strong GC, N=any Σ=sum)
  • TsOverTv
  • W2SOverS2W
  • W2N
  • S2N
  • W2S
  • S2W
  • ΣTs
  • Ts1
  • Ts2
  • ΣTv
  • TvW
  • TvN1
  • TvS
  • TvN2

The main methods are:

  • calcFreq(mutball): calculates the parameters associated with the number of mutations per sequence, in turn it calls various functions including fit(ordinate), which is a wrapper for the non-linear fitting fuction fminsearch (fun,Parm0,x,y,Opt), passing it the function of the Poisson distribution —i.e. if you want to change function tinker with fit(). fminsearch (fun,Parm0,x,y,Opt) is a small function adapted from JMat (GNU licence)
  • calcBias(mutball): calculates the mutational spectrum parameters.
  • Mutagen(): returns a blank mutball object.

So say one wanted to modify the script for personal use to calculate the p-value from a t-test against a given value and return it as an alert. One would have to find or write a t-test function and add it to a local copy of mutationalBias.js. Then to the end of calcBias() just before the return add an alert to pop up with the p-value. Parenthetically, whereas a normal distribution assumption is unavoidable due to the lack of data, it is not at all a good idea and is better to not hazard a guess of the probability, but to resort to other methods (e.g. if the value is within the error range there is no difference).

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