Man pages for nclark-lab/RERconverge
Analysis of Convergence Between Organismal Traits and DNA/Protein Sequences
| adaptivePermulation | Adaptively calculates permulation p-value for a single... |
| asymmRerootingMethod | Calculates ancestral likelihoods of ancestral states for... |
| boxPlotTest | Compares prediction accuracy under different rate models and... |
| calculateCorPermuted | Calculate permulation correlation statistics |
| calculatePermulatedPaths_apply | Calculates the paths for all permulated trees for a list of... |
| char2Paths | turns a named vector of characters into a paths vector to be... |
| char2PathsCategorical | turns a named vector of characters into a paths vector to be... |
| char2TreeCategorical | Creates a categorical trait tree from a set of tip species. |
| click_select_foreground_branches | Interactive click-based function to select foreground... |
| combinePermData | Combines batches of permulations |
| compareRateModels | Performs pairwise likelihood ratio comparisons on a list of... |
| correlateWithBinaryPhenotype | Computes the association statistics between RER from... |
| correlateWithCategoricalPhenotype | Computes the association statistics between RER from... |
| correlateWithContinuousPhenotype | Computes the association statistics between RER from... |
| edgeVars | maps a vector of traits onto a reference tree |
| estimatePhangornTree | Estimate a ML tree from a given topology Uses 'pml' and... |
| estimatePhangornTreeAll | Estimates a ML trees from a given topology for a list of... |
| fastwilcoxGMTall | Performs Wilcoxon Rank-Sum pathway enrichment on pathway... |
| filterByCriteria | Filters a list of rate models based on a boolean expression... |
| fixPseudoroot | pseudoroot trait tree to match the psuedoroot of trees from... |
| foreground2Paths | Creates paths from a set of foreground species |
| foreground2Tree | Creates a binary trait tree from a set of foreground species. |
| foreground2TreeClades | Generates a binary phenotype tree using the list of tip... |
| generatePermulatedBinPhen | Produces binary permulations for a gene |
| generatePermulatedBinPhenSSMBatched | Produces binary SSM permulations for a list of genes |
| getAllCor | Computes the association statistics between RER from... |
| getAllCorExtantOnly | Computes the association statistics between RER from... |
| getAllResiduals | main RER computation function |
| getAncLiks | Returns ancestral likelihoods at each node. Based on code... |
| getBinaryPermulationInputsFromTree | Produces the phenotype inputs for binary permulation... |
| getEnrichPerms | Performs enrichment statistic permulations using existing... |
| getForegroundInfoClades | Generates a binary phenotype tree and foreground clades... |
| getLikelihoodRatio | compute the likelihood ratio from the log likeilhoods of two... |
| getLRnullDistribution | Returns the p value of a likelihood ratio based on the... |
| getMatrixFromAbbr | Gets the matrix form of a rate model from its abbreviation |
| getPermsBinary | Calculates permuted correlation and enrichment statistics for... |
| getPermsBinaryExtantOnly | Calculates permuted correlation and enrichment statistics for... |
| getPermsContinuous | Calculates permuted correlation and enrichment statistics |
| getPermsContinuousExtantOnly | Calculates permuted correlation and enrichment statistics for... |
| getStat | Calculates Rho-signed negative log-base-ten p-value for use... |
| getStatesAtNodes | returns the states at each node corresponding to the state... |
| getStatesFromPhenTree | Returns a list of states in node order from a phenotype tree |
| kwdunn.test | A sped up version of the Kruskal Wallis/Dunn Test |
| makeBinaryPaths | Makes a binary path vector from either a tree of class... |
| matchAllNodesClades | Calculates the clade mappings between the gene tree and the... |
| namePathsWSpecies | Provides names for paths/RERs representing terminal branches... |
| permpvalcor | Calculates correlation permutation pvals from output of... |
| permpvalenrich | Calculates enrichment permutation pvals from output of... |
| permutevec | Generates a permuted continuous phenotype given an observed... |
| plotPositivesFromPermulations | Plots changes in number of statistically significant rate... |
| plotRers | Plot the residuals reflecting the relative evolutionary rates... |
| plotTreeCategorical | Plot a phenotype tree generated by 'char2TreeCategorical'... |
| plotTreeHighlightBranches | Plot the provided tree, (optionally) rerooted, with specified... |
| pruneTree | wrapper around 'drop.tip' |
| read.gmt | Reads pathway data from a gmt-formatted file from GSEA-MSigDB |
| readTrees | reads trees from a 2 column , tab seperated, file The first... |
| RERconverge | RERconverge |
| returnRersAsNewickStrings | Produce a vector of newick strings representing gene trees... |
| returnRersAsTree | Produce a gene tree with branch lengths representing RERs and... |
| returnRersAsTreesAll | Produce a multiPhylo object of all gene trees with branch... |
| Root | the function root from ape modified to return additional... |
| searchRateModels | iteratively searches for simpler rate models that still... |
| simBinPheno | Generates a permulated phylogenetic tree with specified... |
| simBinPhenoCC | Produces one CC binary permulation for a gene |
| simBinPhenoCCmidpoint | Produces one CC binary permulation for a gene using midpoint... |
| simBinPhenoRank | Produces one binary permulation based on ranking of simulated... |
| simBinPhenoSSM | Produces one SSM binary permulation for a gene |
| simBinPhenoVec | Generates a permulated phenotype vector whose phylogeny... |
| simpermvec | Generates a permulated continuous phenotype given an observed... |
| simulatevec | Generates a simulated continuous phenotype given an observed... |
| tree2Paths | Generate a phenotype paths vector from a phenotype tree |
| tree2PathsClades | A modification of the tree2Paths function that takes in... |
| treePlotNew | Plot 'tree' with branch labels colored in a heatmap based on... |
| treePlotRers | Plot a cladogram with RERs shown as either labels... |
| visCompareTwoRateModels | Visually compare the results of two rate models by plotting... |
