Analysis of Convergence Between Organismal Traits and DNA/Protein Sequences

char2Paths | turns a named vector of characters into a paths vector to be... |

click_select_foreground_branches | Interactive click-based function to select foreground... |

correlateWithBinaryPhenotype | 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 |

fastwilcoxGMTall | Performs Wilcoxon Rank-Sum pathway enrichment on pathway... |

foreground2Paths | Creates paths from a set of foreground species |

foreground2Tree | Creates a binary trait tree from a set of foreground species. |

getAllCor | Computes the association statistics between RER from... |

getAllResiduals | main RER computation function |

getStat | Calculates Rho-signed negative log-base-ten p-value for use... |

makeBinaryPaths | Makes a binary path vector from either a tree of class... |

namePathsWSpecies | Provides names for paths/RERs representing terminal branches... |

plotRers | Plot the residuals reflecting the relative evolutionary rates... |

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 |

tree2Paths | Generate a phenotype paths vector from a phenotype tree |

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