README.org

TreeWAS - Genetic risk profiles

---

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 here.

Demo

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
)

Install

library(devtools)

install_github("mcveanlab/TreeWASDir")