In order to test treeWAS tool described in the paper we launched the program twice using gene presence-absence matrix of the bacteria Neisseria meningitidis (file genematrix.txt in the root folder) and its phenotype vector (file phenotypes_2.txt). The R code written to run treeWAS is in R_code.txt file (two launches differ by a tree reconstruction method: BIONJ or NJ). Folder "data" contains files returned by treeWAS after two launches. We were interested in simultaneous score estimation reproducibility and recounted it with Python code (file treewas_reproduce_project.ipynb). Our code uses trees, phenotype ancestor reconstruction and genotype ancestor reconstruction built by treeWAS to identify simultaneous score values and compares it with treeWAS result. All plots returned by treeWAS we were interested in are in 'plots' folder.
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Test of treeWAS tool described in the paper "A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination" (Caitlin Collins, Xavier Didelot, 2018, PLOS Computational Biology).
Reproducibility-FBB-MSU/treeWAS
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Test of treeWAS tool described in the paper "A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination" (Caitlin Collins, Xavier Didelot, 2018, PLOS Computational Biology).
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