+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

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