chr1swallace

## download https://www.t1dbase.org/downloads/protected_data/GWAS_Data/hg19_gwas_t1d_barrett_4_18_0.gz
## you will need to create a login!
## Then...
x <- read.table("hg19_gwas_t1d_barrett_4_18_0.gz",sep="\t",skip=1,as.is=TRUE)
colnames(x) <- c("snp","Chr","Pos","PValue","OR","kk")

## libraries
library(ggplot2)
library(cowplot) # nicer ggplot theme

chr1swallace

# replace "gantt.csv" with path to wherever your .csv file is stored
x <- read.table("gantt.csv",sep=",",as.is=TRUE, header=TRUE) # read data

## look at what we read, check it makes sense
head(x)

## make sure dates are recognised as such
x$Start <- as.Date(x$Start)
x$End <- as.Date(x$End)

chr1swallace

##' Fit a specific two Guassian mixture distribution
##'
##' Assumes Z ~ N(0,1) with prob pi0,
##' Z ~ N(0,1+sigma^2) with prob 1-pi0
##'
##' Aims to estimate sigma^2 and pi0.
##'
##' @title fit.em
##' @param Z numeric vector of observed data
##' @param s2 initial value for sigma^2