Files in caitiecollins/treeWAS
Run phylogenetic tree-based GWAS

.Rbuildignore
.gitignore
DESCRIPTION
LICENSE.txt
NAMESPACE
R/beeswarm.plot.R R/coalescent.sim.R R/coalescent.tree.sim.R R/fitch.R R/fwd.coalescent.sim.R R/fwd.phen.sim.R R/fwd.plot.prob.phen.R R/fwd.snp.sim.R R/get.sig.snps.R R/heatmap.DNAbin.R R/phen.sim.R R/plot.phen.R R/plot.sig.snps.R R/readCFML.R R/reconstruct.R R/simTest.R R/simultaneous.test.R R/simultaneous.test.epi.R R/snp.sim.Q.R R/snp.sim.R R/subsequent.test.R R/terminal.test.R R/terminal.test.epi.R R/tree.reconstruct.R R/treeWAS.R R/utils.R README.md
data/dist_0.01.rda
data/dist_0.05.rda
data/dist_0.1.rda
data/dist_0.2.rda
data/dist_0.25.rda
data/dist_0.rda
data/phen.cont.rank.rda
data/phen.cont.rda
data/phen.plot.col.rda
data/phen.rda
data/phen.reconstruction.rda
data/snps.assoc.rda
data/snps.rda
data/snps.reconstruction.rda
data/tree.rda
data/treeWAS.example.out.rda
man/asr.Rd man/assoc.test.Rd man/beeswarmPlot.Rd man/coalescent.sim.Rd man/coalescent.tree.sim.Rd man/fwd.coalescent.sim.Rd man/fwd.phen.sim.Rd man/fwd.snp.sim.Rd man/get.ancestral.pars.Rd man/get.assoc.scores.Rd man/get.binary.snps.Rd man/get.fitch.n.mts.Rd man/get.original.loci.Rd man/get.score3.Rd man/get.sig.snps.Rd man/get.tip.order.Rd man/get.unique.matrix.Rd man/ggplotbg.Rd man/heatmap.DNAbin.Rd man/keepFirstN.Rd man/keepLastN.Rd man/manhattan.plot.Rd man/memfree.Rd man/phen.sim.Rd man/plot.phen.Rd man/plot.prob.phen.Rd man/plot.sig.snps.Rd man/print.treeWAS.Rd man/read.CFML.Rd man/removeFirstN.Rd man/removeLastN.Rd man/selectBiallelicSNP.Rd man/set.args.Rd man/simTest.Rd man/simultaneous.test.Rd man/simultaneous.test.epi.Rd man/snp.sim.Q.Rd man/snp.sim.Rd man/subsequent.test.Rd man/table.matrix.Rd man/terminal.test.Rd man/terminal.test.epi.Rd man/tree.reconstruct.Rd man/treeWAS.Rd man/write.treeWAS.Rd
treeWAS.Rproj
vignettes/.build.timestamp
vignettes/figs/Eqn_Legend_genotype.JPG
vignettes/figs/Eqn_Legend_genotype.pdf
vignettes/figs/Eqn_Legend_genotype.png
vignettes/figs/plot_hist_phen.pdf
vignettes/figs/plot_hist_phen.png
vignettes/figs/plot_hist_phen_rank.pdf
vignettes/figs/plot_hist_phen_rank.png
vignettes/figs/plot_hist_simultaneous.pdf
vignettes/figs/plot_hist_simultaneous.png
vignettes/figs/plot_hist_subsequent.pdf
vignettes/figs/plot_hist_subsequent.png
vignettes/figs/plot_hist_terminal.pdf
vignettes/figs/plot_hist_terminal.png
vignettes/figs/plot_manhattan_simultaneous.pdf
vignettes/figs/plot_manhattan_simultaneous.png
vignettes/figs/plot_manhattan_subsequent.pdf
vignettes/figs/plot_manhattan_subsequent.png
vignettes/figs/plot_manhattan_terminal.pdf
vignettes/figs/plot_manhattan_terminal.png
vignettes/figs/plot_tree.pdf
vignettes/figs/plot_tree.png
vignettes/figs/tree_phen_eg.pdf
vignettes/figs/tree_phen_eg.png
vignettes/old/README_10_07_2017.md vignettes/old/ace.tree.cont.IC.pdf vignettes/old/ace.tree.cont.pdf vignettes/old/ace_example.R
vignettes/old/ace_example_phen_R_0.Rdata
vignettes/old/figsunnamed-chunk-12-1.pdf vignettes/old/figsunnamed-chunk-13-1.pdf vignettes/old/figsunnamed-chunk-14-1.pdf vignettes/old/figsunnamed-chunk-15-1.pdf vignettes/old/figsunnamed-chunk-16-1.pdf vignettes/old/figsunnamed-chunk-17-1.pdf vignettes/old/figsunnamed-chunk-7-1.pdf vignettes/old/pagel_example.R
vignettes/old/phen_cont_skewed.Rdata
vignettes/old/phen_cont_skewed_rank.Rdata
vignettes/old/score3_output_example.R vignettes/old/treeWAS Vignette.pdf vignettes/old/treeWAS_example.R
vignettes/old/treeWAS_vignette_files/figure-markdown_strict/unnamed-chunk-10-1.png
vignettes/old/treeWAS_vignette_files/figure-markdown_strict/unnamed-chunk-12-1.png
vignettes/old/treeWAS_vignette_files/figure-markdown_strict/unnamed-chunk-19-1.png
vignettes/old/treeWAS_vignette_files/figure-markdown_strict/unnamed-chunk-20-1.png
vignettes/old/treeWAS_vignette_files/figure-markdown_strict/unnamed-chunk-21-1.png
vignettes/old/treeWAS_vignette_files/figure-markdown_strict/unnamed-chunk-22-1.png
vignettes/old/treeWAS_vignette_files/figure-markdown_strict/unnamed-chunk-23-1.png
vignettes/old/treeWAS_vignette_files/figure-markdown_strict/unnamed-chunk-24-1.png
vignettes/old/treeWAS_vignette_files/figure-markdown_strict/unnamed-chunk-5-1.png
vignettes/old/treeWAS_vignette_files/figure-markdown_strict/unnamed-chunk-8-1.png
vignettes/treeWAS_vignette.Rmd
vignettes/treeWAS_vignette.html
caitiecollins/treeWAS documentation built on April 19, 2019, 4:08 a.m.