These are the MATLAB scripts used for analysis of the fluctuation tests used to measure the mutation rate of S. cerevisiae as described in Lang and Murray, Genetics 2008
The scripts were ported from the original by Toshinori Endo on 2020.12.21. Though reasonable care had been taken, the codes are provided as-is with no guarantee.
Input: data from fluctuation assay. Output: most likely value of m given the data. Command: findMLm(data) This program requires the following programs to run: scoreData, generateLD.
Input: data from fluctuation assay. Output: most likely values of m and d given the data. Command: findMLmTwoParameter(data) This program requires the following programs to run: scoreDataTwoParam, generateLD, generatePO, generateTwoParam.
Input: data from fluctuation assay and m. Output: -log probability of observing the data given m. Command: scoreData(data, m) This program requires the following program to run: generateLD.
Input: data from fluctuation assay, m, and d. Output: -log probability of observing data given m and d. Command: scoreDataTwoParam(data, m, d) This program requires the following programs to run: generateLD, generatePO, generateTwoParam.
Input: m, and max. Output: The Luria-Delbruck distribution from 0 to max with parameter m. Command: generateLD(m, max)
Input: lambda, and max. Output: The Poisson distribution from 0 to max with parameter lambda. Command: generatePO(lambda, max)
Input: m, d, and max. Output: The combined Luria-Delbruck and Poisson distribution from 0 to max with parameters m and lambda = m x d. Command: generateTwoParam(m, d, max) This program requires the following programs to run: generateLD, generatePO.
Input: m, number of samples. Output: Random variables from the Luria-Delbruck distribution with parameter m. Command: sampleLD(m, samples) This program requires the following program to run: generateLD.
Input: m, number of samples. Output: Random variables from a combined Luria-Delbruck and Poisson distribution with parameters m and lambda = m x d. Command: sampleTwoParam(m, d, samples) This program requires the following programs to run: generateLD, generatePO, generateTwoParam.
Input: data from fluctuation assay. Output: sum of the squared differences between the cumulative distribution of the data and the cumulative Luria-Delbruck distribution with parameter m determined from the data. Command: SSDScore(data) This program requires the following programs to run: findMLm, scoreData, generateLD.
Input: data from fluctuation assay. Output: sum of the squared differences between the cumulative distribution of the data and the cumulative combined Luria-Delbruck and Poisson distribution with parameters m and lambda = m x d determined from the data. Command: SSDScoreTwoParam(data) This program requires the following programs to run: findMLmTwoParam, scoreDataTwoParam, generateLD, generatePO, generateTwoParam.