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This is the code repository for my master thesis: Inferring natural selection from pool-sequencing allele frequency data -- an applied statistical genetics project on drought tolerance in Brassica napus at FiBL

Structure

~/plots: all figures in the thesis

~/renv: R package environment

~/scripts contains all R code written and used for the thesis

• combine_replicates.R: all data preprocessing
• darmor2shengli.R: mapping of SNP positions found in the GWAS literature to the reference genome used for genotyping our data
• allele_frequency_means.R: all descriptive statistics per generation, per haplotype, and per chromosome
• run_equaltest.R: run the pairwise testing approach from section 4.1 with (zero-inflated) negative binomial model fits and likelihood ratio test across all haplotypes
• run_betareg.R: run the second extension using beta regression from section 4.2
• evaluate_equaltest.R: evaluate the results produced by run_equaltest.R for section 5.1.2
• evaluate_betareg.R: evaluate the results produced by run_betareg.R for section 5.1.3
• figures.R: code producing all figures used in the thesis
• functions: a directory containing R scripts with all functions called by the run_*.R and evaluate_*.R scripts
  • preprocessing_functions.R: functions used for preprocessing in combine_replicates.R and for preprocessing the meteorological data as described in section 3.2.4
  • equaltest_functions.R: functions used in scripts *equaltest.R
  • betareg_functions.R: functions used for scripts *betareg.R
  • plot_functions.R: functions used in figures.R
  • helper_functions.R: convenience functions used throughout