Man pages for caitiecollins/treeWAS
Phylogenetic tree-based microbial GWAS
| asr | Ancestral state reconstruction |
| assoc.test | Run a test of association between SNPs and a phenotype. |
| beeswarmPlot | Beeswarm-and-Box-Plot. |
| coalescent.sim | Simulate a tree, phenotype, and genetic data. |
| coalescent.tree.sim | Short one-phrase description. |
| dist_0 | Nsubs per site with no recombination (R = 0; M = 0.01). |
| dist_0.01 | Nsubs per site with limited recombination (R = 0.01; M =... |
| dist_0.05 | Nsubs per site with recombination (R = 0.05; M = 0.01). |
| dist_0.1 | Nsubs per site with recombination (R = 0.1; M = 0.01). |
| dist_0.2 | Nsubs per site with considerable recombination (R = 0.2; M =... |
| dist_0.25 | Nsubs per site with considerable recombination (R = 0.25; M =... |
| fwd.coalescent.sim | Short one-phrase description. |
| fwd.phen.sim | Simulate a phenotype, from root to tips. |
| fwd.snp.sim | Short one-phrase description. |
| get.ancestral.pars | Ancestral sequence reconstruction via parsimony |
| get.assoc.scores | Get significant SNPs, according to a given test of... |
| get.binary.snps | Reduce a genetic data matrix to only necessary columns. |
| get.fitch.n.mts | Caclulate parsimony scores. |
| get.original.loci | '(read.CFML+)' Get original sequence positions of polymorphic... |
| get.score3 | Short one-phrase description. |
| get.sig.snps | Get significant SNPs, according to a given test of... |
| get.tip.order | Get the order of the tip labels of a phylogenetic tree as... |
| get.unique.matrix | Get unique rows/columns of a matrix with an index vector. |
| ggplotbg | Mimic ggplot2 Background |
| heatmap.DNAbin | Short one-phrase description. |
| keepFirstN | Truncate to keep only the _first_ N characters. |
| keepLastN | Truncate to keep only the _last_ N characters. |
| manhattan.plot | Manhattan Plot |
| memfree | Get the current amount of available memory. |
| pair.tests | Pairwise tests for categorical phenotypes |
| phen | A binary phenotype. |
| phen.cont | A continuous phenotype. |
| phen.cont.rank | A rank-transformed continuous phenotype. |
| phen.plot.col | Phenotypic tree-colouring schemes. |
| phen.reconstruction | The ancestral state reconstruction of a binary phenotype. |
| phen.sim | Short one-phrase description. |
| plot_phen | Plot the states of a phenotype or genotype along a... |
| plot_prob_phen | Plot the probability of association, given 'p' and... |
| plot_sig_snps | Plot null distribution and significant sites. |
| print.treeWAS | Print 'treeWAS' output. |
| read.CFML | Convert ClonalFrameML output. |
| removeFirstN | Truncate to remove all of the _first_ N characters. |
| removeLastN | Truncate to remove all of the _last_ N characters. |
| selectBiallelicSNP | Short one-phrase description. |
| set.args | Set a list of arguments. |
| simTest | Simulation Testing. |
| simultaneous.test | Simultaneous test |
| simultaneous.test.epi | Test for association between genetic loci with Score 2. |
| snps | A genetic data matrix. |
| snps.assoc | The phenotypically-associated sites in the 'snps' matrix. |
| snp.sim | Short one-phrase description. |
| snp.sim.Q | Aternative SNPs simulation fn. |
| snps.reconstruction | The ancestral state reconstruction of a genetic data matrix. |
| subsequent.test | Subsequent test |
| table.matrix | Cross-tabulate the rows or columns of a matrix. |
| terminal.test | Terminal test |
| terminal.test.epi | Test for epistasis between genetic loci with Score 1. |
| tree | A phylogenetic tree. |
| tree.reconstruct | Short one-phrase description. |
| treeWAS | Phylogenetic tree-based GWAS for microbes. |
| treeWAS.example.out | Example output of treeWAS. |
| write.treeWAS | Write 'treeWAS' output to a CSV file. |
