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library(ggdendro) | |
library(ggplot2) | |
library(reshape) | |
library(grid) | |
library(gtable) | |
## colours, generated by | |
## library(RColorBrewer) | |
## rev(brewer.pal(11,name="RdYlBu")) | |
my.colours <- c("#313695", "#4575B4", "#74ADD1", "#ABD9E9", "#E0F3F8", "#FFFFBF", |
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library(nnet) | |
nsnp <- 3 | |
simdata <- function(n) { | |
X <- matrix(pmin(abs(rnorm(n*nsnp)),3),nrow=n) | |
p <- rbinom(n, 1, X[,1]/3) | |
q <- rbinom(n, 1, X[,nsnp]/3) | |
Y <- ifelse(p>0, 1, ifelse(q>0, 2, 0)) |
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coloc.bayes.3t <- function(df1,snps=setdiff(colnames(df1),response),response="Y",priors=list(rep(1,14)),r2.trim=0.99,thr=0.005,quiet=TRUE) { | |
#we consider all models which contain at most 1 snp for each of the three traits | |
snps <- unique(snps) | |
n.orig <- length(snps) | |
if(n.orig<2) | |
return(1) | |
prep <- prepare.df(df1, snps, r2.trim=r2.trim, dataset=1, quiet=quiet) | |
df1 <- prep$df | |
snps <- prep$snps | |
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library(MASS) | |
data<-mvrnorm(n=100, mu=c(1,2), Sigma=matrix(c(1,0.5,0.5,1),2)) | |
colnames(data) <- c("x","y") | |
var(data) | |
cor(data) | |
data[,"x"] <- data[,"x"] + 3 | |
var(data) # unchanged | |
cor(data) # unchanged |
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library(snpStats) | |
best <- cond.best(X,Y, family=family) | |
while(length(newbest <- cond.best(X, Y, best, family=family))) | |
best <- c(best,newbest) | |
cond.best <- function(X,Y,best=NULL,p.thr=1e-6, ...) { | |
if(is.null(best)) { | |
cond <- snp.rhs.tests(Y ~ 1, snp.data=X, data=data.frame(Y=Y, | |
row.names=rownames(X)), ...) | |
p.thr <- 1 |
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##' 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 |
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# 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) |
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## install packages using the following | |
## install.packages("devtools") | |
## library(devtools) | |
## install_github("ropensci/rorcid") | |
## install.packages(c("tm","wordcloud")) | |
## load libraries | |
library(rorcid) | |
library(wordcloud) |
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## 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 |
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## sharing parameter, largish, so we expect to see a big enough difference to check if working | |
S <- 100 | |
prior.bin.fn <- function(nT1,s=100,mT1=3) { | |
dbinom(nT1,size=s,prob=mT1/s)/choose(s,nT1) | |
} | |
bothpp <- function(data) { | |
ss1 <- strsplit(data$t1.str,"%") | |
ss2 <- strsplit(data$t2.str,"%") | |
data$overlap <- sapply(1:nrow(data), function(i) |
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