+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")