explodecomputer

#!/bin/bash
 
#PBS -N extractdata
#PBS -o extractdata-output
#PBS -e extractdata-error
#PBS -t 1-23
#PBS -l walltime=24:00:00
#PBS -l nodes=1:ppn=2
#PBS -S /bin/bash
 

explodecomputer

#!/bin/bash

cd /panfs/panasas01/shared/alspac/studies/latest/alspac/genetic/variants/arrays/gwas/imputed/1000genomes/released/27Feb2015/data/derived

mkdir -p ~/updated_ids
mkdir -p ~/updated_ids/kinships
mkdir -p ~/updated_ids/principal_components/all
mkdir -p ~/updated_ids/principal_components/unrelateds
mkdir -p ~/updated_ids/exclusion_ids
mkdir -p ~/updated_ids/unrelated_ids

explodecomputer

#!/bin/bash

for i in {1..9}
do
	plink1.90 --bfile ~/data/alspac_1kg/data/genotypes/bestguess/subset_maf0.01_info0.8/data_chr0${i} --extract ~/data/1kg_scratch/hapmap3_autosome.snplist --make-grm-bin --out data_chr0${i} --maf 0.01
done

for i in {10..22}
do
	plink1.90 --bfile ~/data/alspac_1kg/data/genotypes/bestguess/subset_maf0.01_info0.8/data_chr${i} --extract ~/data/1kg_scratch/hapmap3_autosome.snplist --make-grm-bin --out data_chr${i} --maf 0.01

explodecomputer

setwd("/I/DON\'T/KNOW/YOUR/COMPUTER")


# Install pdftotext from here: 
# http://mac.softpedia.com/get/Word-Processing/pdftotext-Installer-Package.shtml


# Find pdf files in a directory
get_pdf_files <- function(wd="./")
{

explodecomputer

two_sample_iv <- function(b_exp, b_out, se_exp, se_out, n=10000)
{
	b <- sum(b_exp*b_out / se_out^2) / sum(b_exp^2/se_out^2)
	se <- sqrt(1 / sum(b_exp^2/se_out^2))
	pval <- pt(b / se, df = n, low=FALSE)
	return(list(b=b, se=se, pval=pval))
}

two_sample_iv_delta <- function(b_exp, b_out, se_exp, se_out, n=10000, cov=1)
{

explodecomputer

#!/bin/bash

# From https://forums.plex.tv/index.php/topic/153446-this-server-is-not-powerful-enough-to-convert-video/page-3

cd /var/lib/plexmediaserver/Library/Application\ Support/Plex\ Media\ Server/Plug-ins/WebClient.bundle/Contents/Resources/js

sudo sed -i 's/validateTranscoder:function(e,t){if/validateTranscoder:function(e,t){return false;if/g' plex.js

explodecomputer

calculate_mean_squared_error <- function(dati, samplesize, numberofbootstraps)
{
	squared_error <- array(0, numberofbootstraps)
	mean_dati <- mean(dati)
	for(i in 1:numberofbootstraps)
	{
		squared_error[i] <- (mean_dati - mean(sample(dati, samplesize)))^2
	}
	return(mean(squared_error))
}

explodecomputer

library(MASS)


#' Simulate two traits with shared genetic and environmental effects
#'
#' @param nid sample size
#' @param  nsnp number of snps
#' @param  hsq1 h2 of trait 1
#' @param  hsq2 h2 of trait 2
#' @param  rg genetic correlation

explodecomputer

library(dplyr)

arguments <- commandArgs(T)
splits <- as.numeric(arguments[1])
outdir <- arguments[2]
savefile <- arguments[3]

l <- list()
for(i in 1:splits)
{

explodecomputer

arguments <- commandArgs(T)

codefile <- arguments[1]
bimfile <- arguments[2]
chr <- arguments[3]

codes <- read.table(codefile, colClass=c("character", "numeric", "character", "character"))
index <- codes$V1 == "."
codes$V1[index] <- paste("chr", chr, ":", codes$V2[index], sep="")
dim(codes)