treatmentResponseDiallel

Summary

This package is used for the analysis of treatment-response phenotypes in a diallel study on the host response to influenza (Maurizio et al., 2018, G3). It can be installed and used in conjunction with code and specific dependencies housed at https://github.com/mauriziopaul/flu-diallel.

A static version of the data, software, and scripts used to analyze this data upon submission is available at DOI: 10.5281/zenodo.293015.

Installation

You can install treatmentResponseDiallel using the following code.

First, in R:

install.packages(c('coda', 'corpcor','R.oo'))

Additional dependencies are located here https://github.com/mauriziopaul/flu-diallel/tree/master/packages. Then, on the command line (for Mac, replacing * with the version number):

R CMD install BayesDiallel_*.tar.gz;
R CMD install BayesSpike_*.tar.gz;
R CMD install cmdline_*.tar.gz;
R CMD install WVmisc_*.tar.gz;
R CMD install configfile_*.tar.gz;

Then, from R:

# install.packages("devtools")
devtools::install_github("mauriziopaul/treatmentResponseDiallel")
library("treatmentResponseDiallel")

Related Software

1. BayesDiallel http://valdarlab.unc.edu/software/bayesdiallel/BayesDiallel.html

2. Diploffect http://valdarlab.unc.edu/software/diploffect/index.html

More Information

For more information about my research interests, please visit https://mauriziopaul.github.io/. To learn more about research in the Heise and Valdar labs, please visit and https://unclineberger.org/people/mark-heise and http://valdarlab.unc.edu.

Key References

Maurizio PL, Ferris MT, Keele GR, Miller DR, Shaw GD, Whitmore AC, West A, Morrison CR, Noll KE, Plante KS, Cockrell AS, Threadgill DW, Pardo-Manuel de Villena F, Baric RS, Heise MT & Valdar W (2018) Bayesian diallel analysis reveals Mx1-dependent and Mx1-independent effects on response to influenza A virus in mice. G3: Genes, Genomes, Genetics 8(2):427-445. 10.1534/g3.117.300438. PMID:29187420.

Maurizio PL & Ferris MT (2017) “Chapter 28: The Collaborative Cross Resource for Systems Genetics Research of Infectious Diseases.” Methods in Molecular Biology: Systems Genetics – Methods and Protocols. Springer Science+Business Media, New York, NY. Klaus Schughart and Robert W. Williams (eds.) 1488:579-596. eBook ISBN: 978-1-4939-6427-7, hardcover ISBN: 978-1-4939-6425-3. doi: 10.1007/978-1-4939-6427-7_28. PMID:27933545.

Zhang Z, Wang W, Valdar W (2014) Bayesian modeling of haplotype effects in multiparent populations. Genetics 198(1):139-56. doi: 10.1534/genetics.114.166249

Crowley JJ, Kim Y, Lenarcic AB, Quackenbush CR, Barrick C, Adkins DE, Shaw GS, Miller DR, Pardo Manuel de Villena F, Sullivan PF, Valdar W (2014) Genetics of adverse reactions to haloperidol in a mouse diallel: A drug-placebo experiment and Bayesian causal analysis. Genetics 196(1):321-47. doi: 10.1534/genetics.113.156901

Ferris MT, Aylor DL, Bottomly D, Whitmore AC, Aicher LD, Bell TA, Bradel-Tretheway B, Bryan JT, Buus RJ, Gralinski LE, Haagmans BL, McMillan L, Miller DR, Rosenzweig E, Valdar W, Wang J, Churchill GA, Threadgill DW, McWeeney SK, Katze MG, Pardo-Manuel de Villena F, Baric RS, Heise MT (2013) Modeling host genetic regulation of influenza pathogenesis in the Collaborative Cross. PLoS Pathogens 9(2):e1003196. doi: 10.1371/journal.ppat.1003196

Lenarcic AB, Svenson KL, Churchill GA, Valdar W (2012) A general Bayesian approach to analyzing diallel crosses of inbred strains. Genetics 190:413-435. doi: 10.1534/genetics.111.132563