Vignette modifications and bug fix for missing data preprocessing #2
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…ing out information on SNPs in the same LD block.
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This vignette was tremendously helpful in implementing the GADGETS algorithm. Based on how the authors have modified their analysis pipeline over time, some clarity was added about what to do when running the global test for the network plot versus when just running the visualization with the top few fitness scores. Some sections were rearranged to go along with this change. A couple just-in-case lines were added to the .gitignore, depending on what happens when people run the .Rmd to make the vignette (if the "unlink" is not reached at the end of the vignette, or if the knitted HTML files are not deleted).
Due to some results that arose when including single-SNP risk sets, some clarity was added with feedback from authors on genetic distance, determining linkage disequilibrium, and what happens when SNPs in the same epistatic set are on the same linkage block.
A couple of minor grammatical changes were made, and a spelling correction.
Bug fixed in
preprocess.genetic.data. Previouslycase.datawas modified in-place, affecting the next line when settingcomp.datato -9 when missing.