TESS3r_SNPs

R-markdown script for spatial population genetic structure analysis with Tess3r (v1.1.0; https://github.com/bcm-uga/TESS3_encho_sen).

This series of R scripts imports genotype data from a .csv file with 1 column for sample ID's and 2 columns per locus for genotypes, and a file of at least one stratification scheme and sample geographic locations (latitude and longitude in decimal format), converts the data to a Gtypes object that combines the sample information with the genotypes, and then conducts several analyses from Tess3r.

Steps:

1. load genotype data and stratification schemes from .csv files.
2. Create g-types object merging the data with the selected stratification scheme
3. remove samples with no latitude or longitide data (required for TESS) and monomorphic loci (in the selected strata). A file with the list of monomorphic loci that were removed is saved.
4. summarize stratified data and output summary files for strata, loci and samples.
5. generate a map showing the data points for the selected stratification scheme.
6. reformat the data for input to Tess; Convert the gtypes object to a structure-formatted file, then to a GENIND object, then to Tess format (numerical alleles).
7. run Tess3 for a specified range of k (one to max.k) and number of iterations.
8. output cross-validate scores for each k to infer optimal number of populations.
9. visualize admisture proportions for each K as a barplot
10. map spatial interpolation of ancestry coefficients
11. ouptut histogram of p-values for specified k (this should be modified to do for all values of k)
12. output manhattan plot to show outlier p-values for Fst
13. save all data to a rdata file.
14. knit to pdf, html or docx file.