marlonecobos/Anopheles

Anopheles Genome Environment Associations

This repository contains a comprehensive compilation of code and expalantory visualization associated with the paper: Genome-environment Association Methods Comparison Indicates Omnigenic Adaptation to Ecological Niche in Malaria Vector Mosquitoes

Visualizations of processes described in the paper

Confirm convergence of BayeScEnv MCMC chains using the R package coda

• For all 25 datasets (5 variables x 5 chromosome arms):

  https://devonderaad.github.io/Anopheles/run.bayescenv/bayescenv.confirm.convergence.html

Optimize mtry for each independent r2VIM run

• Example for humidity ~ chromosome 2L:

  https://devonderaad.github.io/Anopheles/r2vim/optimize.mtry/hum.2L.r2vim.optimize.html

Perform 'repeated correlations' simple, intuitive GEA testing approach

• Perform each correlation, store relevant values, explore significance cutoffs:

  https://devonderaad.github.io/Anopheles/run.repeated.correlations/repeated.correlations.testing.html

Vetting process using allele frequency patterns from independent genetic sampling efforts

• Entire process can be viewed here, including visualizations of the resulting classifications showing intuitive usefulness of this process:

  https://devonderaad.github.io/Anopheles/vetting/simple.vetting.all.GEAs.html

Testing the effect of spatial and genomic autocorrelation of dependent variable on GEA results

• The process of calculating correlation matrices, mantel tests, and evaluating the effect on number/proportion of GEA outliers can be viewed here:

  https://devonderaad.github.io/Anopheles/test.correlations/test.corrs.html

Identify sets of genes associated with each outlier SNP dataset, and test for significant overrepresentation of the a priori identified desiccation-tolerance candidate genes from Ayala et al. (2019)

• This process can be viewed and reproduced from this markdown:

  https://devonderaad.github.io/Anopheles/gene.association/gene.matching.ayala.overrep.testing.html

Access candidate gene datasets

• All 20 candidate gene and outlier SNP datasets generated here can be directly accessed by following:

  https://github.com/DevonDeRaad/Anopheles/tree/master/candidate.gene.datasets