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data
data
 
 
plots
plots
 
 
recomb_rates
recomb_rates
 
 
reports
reports
 
 
results
results
 
 
.gitignore
.gitignore
 
 
Medicago_MDS.R
Medicago_MDS.R
 
 
Medicago_PCA_win104.R
Medicago_PCA_win104.R
 
 
Medicago_VCF_recode.py
Medicago_VCF_recode.py
 
 
Medicago_distance_all_chr.R
Medicago_distance_all_chr.R
 
 
Medicago_recode_and_cov.R
Medicago_recode_and_cov.R
 
 
README.md
README.md
 
 
compare-parameter-runs.R
compare-parameter-runs.R
 
 
example-run-summary.html
example-run-summary.html
 
 
medicago_data_setup.Rmd
medicago_data_setup.Rmd
 
 
medicago_data_setup.html
medicago_data_setup.html
 
 
medicago_missingness_win104.R
medicago_missingness_win104.R
 
 
run_on_medicago.R
run_on_medicago.R
 
 
skeleton.pbs
skeleton.pbs
 
 
small_skeleton.pbs
small_skeleton.pbs
 
 
summarize_run.Rmd
summarize_run.Rmd
 
 

README.md

In this directory:

  • data/ - Where the raw data goes.

  • medicago_data_setup.html - some initial summaries of the data

  • medicago_data_setup.Rmd - the code that produced those summaries

  • run_on_medicago.R - computes local PC coordinates and MDS coordinates.

  • reports/ - Summary reports showing the results of running the algorithm with different parameter combinations (e.g., window choice; number of PCs) on the data.

  • summarize_run.Rmd - templated report used to produce these.

  • compare-parameter-runs.R - postprocessing to compare different parameter combinations.

First-round analyses (without using the R package):

  • plots
  • Medicago_distance_all_chr.R
  • Medicago_MDS.R
  • Medicago_PCA_win104.R
  • Medicago_recode_and_cov.R