BakrAwa_aDNA

Custom scripts to perform downstream analyses of qpWave and outgroup f3-statistic tests.

Analysis Scripts

This repository contains the R code used to generate the statistical results and figures.

File Descriptions

• qpWave_Permutation_Enrichment_Test.R:

  • Purpose: Tests for significant clade enrichment between the target individual and individuals from the surrounding meta-regions.
  • Input: Processed qpWave RDS files and metadata maps.
  • Output: Enrichment statistics tables for ChL-EBA, EBA-LBA, and IA-Hist periods.

• Bayesian_GLM_PopStruct_Correction.R:

  • Purpose: Runs a Bayesian GLM (MCMCglmm) to predict significant connections to the surrounding meta-regions while controlling for genetic structure.
  • Usage: Designed to be run via command line (e.g., Rscript Bayesian_GLM_Kinship_Correction.R <Individual_ID>).
  • Output: Diagnostic plots (Trace, PPC, ROC) and summary tables of Log-Odds and genetic variance.

• Within_Region_F3_Diversity_Analysis.R:

  • Purpose: Assesses genetic homogeneity within meta-regions.
  • Method: Uses 1 - F3 as a dissimilarity metric and performs betadisper analysis (multivariate homogeneity of groups dispersions).
  • Output: Violin plots, heatmaps, and statistical test results (ANOVA/Permutation).