I´m searching an R package or command line program to calculate heterozygosity-excess (similar to BOTTLENECK, Piry et al. 1999) and m-ratio (Garza and Williamson, 2001) tests for population bottlenecks based on microsatellites.
Would be great if anybody has an idea about that as I have lots of datasets to work on.
Hi Martin,
The R package diveRsity may be useful for this, specifically the basicStat function which will do Hardy-Weinberg Equilibrium tests to look at homozygosity/heterozygosity excesses. Alternatively, the Hwxtest R package might also do the job. More information on these is available in the links below.
Cheers,
ML
https://cran.r-project.org/web/packages/diveRsity/diveRsity.pdf
https://cran.r-project.org/web/packages/HWxtest/HWxtest.pdf
A command line program was developed for the M ratio test. https://swfsc.noaa.gov/textblock.aspx?Division=FED&id=3298
More information on these is available in the links below. i hope this help
Hi everyone and thanks for the answers. Unfortunately, there is no solution so far:
@ Monal : The critical point is the simulation of data under different microsatellite mutation models, which neither of the packages does. This is important to compare the empirical heterozygosity excess to simulated values to get an insight about the likelihood of the data given a certain mutation model.
@ Erin: It is indeed a command line program, however it asks you questions and forces an interactive use which makes it impossible to use it via R or loops to run over a large number of datasets
@ Semir: Thanks for that, but my french didn´t improve much since high school
There are methods of responding to command line prompts within a script. I haven't done it in R but using Perl you could write a loop that includes a response to a question prompt to STDOUT. Something like : http://stackoverflow.com/questions/7852627/when-executing-a-command-in-a-perl-script-can-perl-respond-to-a-stdout-request-p
Alternatively, ask the authors of the M ratio test for their source code?
Hi Erin,
thanks for the link,that´s exactly what I need. And you´re right, I may also just ask the authors for the code.
Dear Martin,
You can use the command line version of Arlequin (i.e., arlsumstat) to calculate the M ratio. I don't know if there is a command line program or R package implementing the heterozygosity excess test. However, you can try to implement manually in R the formulas allowing to calculate the heterozygozities expected at the mutation-drift equilibrium for a given number of alleles and number of samples (ex. formula for the SMM in Kimura & Ohta 1975, PNAS, 72:2761-2764).
Then, you can use other R packages for calculate the observed heterozygosity, and compare the observed vs the expected values in R.
Take a look at this article : Genetic Bottlenecks Driven by Population Disconnection (Broquet et al 2009 Cons Biol 24(6):1596-605); I think that the authors did something like this.
Cheers,
Ivan
Hi Martin,
I just came across your question about M ratio tests and calculation of critical M in R and wondered if you had any luck figuring that out? I'm trying to do the same thing and would be grateful if you could pass on any details if you've been successful.
Thanks, Amanda
Hi Amanda,
strataG provides a function to measure the M-Ratio but doesn´t do simulations to calculate the critical M. The simulations can be done in ms / simcoal instead. I think there is no program in R that can do everything.
Best,
Martin
Hi Martin,
I am also trying to calculate M ratio and critical M values for a large number of (simulated) populations. I have microsatellite genotypes for 1000 populations within each genepop formatted file. I was able to use strataG to calculate the m-ratio for a genepop file that had only one population in it, but I can't figure out a way to do it when I have multiple populations in the same file. To run the single population file, I first converted my genepop file to a genind file with the adgenet package and then to a gtypes object with strataG. However, when I try to convert the multiple population genepop file into a genind file, it doesn't preserve the separate populations, so the results are wrong. Not sure if you ran into a similar issue with your data sets, but I thought I'd check to see if you have any solutions just in case!
Thanks!
Danielle
Hi Danielle,
this seems like a problem you could ask the adagenet maintainers. I never had that problem.
Best,
Martin
Hello,
Several articles perform M-ratio and Mc with the executables M_P_VAL and CRITICAL_M. But I couldn't find them on any page. Could someone share these executables or know where I can find them? Thank you!
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