#+TITLE: TreeWAS - Genetic risk profiles

#+AUTHOR: Adrian Cortes

#+email: adrcort@gmail.com

#+INFOJS_OPT: 

#+BABEL: :session *R* :cache yes :results output graphics :exports both :tangle yes 

#+EXPORT_SELECT_TAGS: export

#+EXPORT_EXCLUDE_TAGS: noexport

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This repository contains R code to perform TreeWAS analysis and infer genetic risk profiles across UK Biobank phenotype data sets. For a description of the method see preprint [[https://www.biorxiv.org/content/early/2018/07/23/374207][here]].

* Demo

#+NAME: demo

#+BEGIN_SRC R

  library(TreeWASDir)

  HES.data <- load.HES.lk.data()

  pars <- load.pars()

  data <- HES.data$d

  res <- HES.data$res

  snp <- "rs4420638"

  SNP.IDX <- which(res$SNP %in% snp)

  ## Calculate the evidence that the SNP is

  ## associated with at least one term in the

  ## ontology

  lBF <- calc.lBF(

      pars       = pars,

      data.sub   = data[SNP.IDX,,]

  )

  cat("The Tree BF is ",round(lBF,2), "\n")

  ## Calculate the risk profile across the

  ## ontology

  pp <- marginal.posterior.profile(

      pars       = pars,

      data.sub   = data[SNP.IDX,,]

  )

  ## visualise the results. Return a plotly

  treePlot <- drawTree(

      tree           = pars$tree,

      pp             = pp,

      tree_title     = res[SNP.IDX,"SNP"],

      trim_tree_pp   = 0.25

  )

#+END_SRC

* Install

#+NAME: install repository

#+BEGIN_SRC R

  library(devtools)

  install_github("mcveanlab/TreeWASDir")

#+END_SRC