Human-Maize co-evolution project - linguistics analyses

Data and scripts for the linguistics analyses of the human-maize co-evolution project. Scripts are generally sorted into four stages:

1. Generate data

• createDistanceMatrices.R
• createDistanceMatrices_Haynie.R
• generateGlobalGrid.R

2. HPC Scripts

For GWAS

• prepare_GWAS_DATA.SH
• makeGWASbinaryfiles.R
• transpose.awk
• One_hot_encoding.R
• language-gwas.sh

For plotting

• getGenotype.sh
• makeManhattanPlot.R
• submit_makeManhattanPlot.sh

For FEEMS

• prepare_FEEMS_data.sh
• run_FEEMS.py
• submit_run_FEEMS.sh

For regression

• prepare_regression_data.sh
• regressionSNPs.sh
• submit_regressionSNPs.sh

Other analysis

• popGenScripts.sh
• performPCA.R

3. Load data

• languageFunction.R
• loadData.R

4. Analyses

• gwasAnalysis.R
• glottologCentroidValidaation.R
• languageRegression.R

5. Plots

• plotMaps.R
• plotManhattans.R
• makeFigurePlots.R