alexmondaini/Quantitative-Genetics

Master Thesis and publication https://doi.org/10.1002/tpg2.20165

Selection Signatures in CIMMYT’s International Elite Spring and Semi-Arid Wheat Yield Trials

There is a chronological order for this work, which must be followed as new R objects are saved and used for downstream pipeline analysis. Please follow this order:

1. Hapmap Transforms textual hapmap format into numeric matrix
2. Trial Data Cleaning Data preparation from field trials
3. PCA Principal Component Analysis
4. FST Fixation Index Metrics over loci and populations
5. allele_frequencies_populations Estimation of population allele frequencies. Please follow this order script:
   • allele_frequencies_1
   • polishing_data_2
   • kernel_3
   • plot_signatures_selection_4
6. adegenet_dapc Population Structure Analysis

P.S: To know more about this study please see my recent publication: https://doi.org/10.1002/tpg2.20165