| nsnp <- 48 | |
| n <- 1000 | |
| mothers1 <- matrix(rbinom(n*nsnp*2, 1, 0.5), n) | |
| kids1 <- matrix(rbinom(n*nsnp, 1, 0.5), n) | |
| kids2 <- mothers1[, seq(1, 2*nsnp, 2)] | |
| kids <- kids1 + kids2 |
| # Null is true | |
| nsim <- 1000 | |
| p <- matrix(0, nsim, 3) | |
| n <- 1000 | |
| g1 <- rbinom(n, 2, 0.2) | |
| g2 <- rbinom(n, 2, 0.3) | |
| g3 <- rbinom(n, 2, 0.4) | |
| g <- cbind(g1, g2, g3) |
| # Simulate the smoking thing | |
| # SNP influences smoking status | |
| # Smoking status influences income | |
| # Test for association of SNP on income in smokers and non smokers | |
| nsim <- 100 | |
| res <- matrix(0, nsim, 4) | |
| n <- 100000 | |
| for(i in 1:nsim) |
| #!/bin/bash | |
| # name of binary plink filename (excluding .bed/.bim/.fam suffix) | |
| plinkfile="" | |
| # output filename | |
| outname="" | |
| # number of causal variants | |
| nvar=1000 |
A lot of servers use Linux and we need to use a server to run a few specific programmes so let's get familiar with Linux.
First of all, to connect to the server we will use a SSH connection. The idea is that we log in to the remote server from our local computer, so when we are running anything on the server we are using its hardware and infrastructure and our local computer is being used to simply view what is happening remotely and to input commands.
| calc.proprare <- function(nsnp, shape1, eff.func, nid) | |
| { | |
| # Generate allele frequency distribution | |
| mafs <- rbeta(nsnp, shape1, 1) / 2 | |
| # Limit min maf to be function of hypothetical sample size | |
| mafs <- pmax(mafs, 1/(nid*2)) | |
| # Create distribution of effect sizes | |
| eff <- eff.func(mafs) |
| # Sample size of PAPA replication | |
| n <- 149 | |
| # Pvals from first 14 CpGs in PAPA replication | |
| pval <- c(9.6e-6, 7.2e-5, 2.8e-6, 3.7e-5, 4.8e-4, 6.2e-3, 4.6e-6, 1.3e-2, 2.6e-3, 3.8e-4, 3.2e-5, 9.0e-4, 8.8e-5, 8.3e-5) | |
| # Estimate F statistics | |
| qval <- qf(pval, 1, n-1, low=F) |
| #!/usr/bin/env bash | |
| # rmate | |
| # Copyright (C) 2011-2013 by Harald Lapp <[email protected]> | |
| # | |
| # This program is free software: you can redistribute it and/or modify | |
| # it under the terms of the GNU General Public License as published by | |
| # the Free Software Foundation, either version 3 of the License, or | |
| # (at your option) any later version. | |
| # |
This requires Python v2.7 plus the following plugin:
| #!/bin/bash | |
| #PBS -l walltime=24:00:00,nodes=1:ppn=1 | |
| #PBS -o output.file | |
| #PBS -me | |
| #PBS -S /bin/bash | |
| set -e | |
| module add apps/vcftools-0.1.12b | |
| export PERL5LIB=/cm/shared/apps/VCFTOOLS-0.1.12b/vcftools_0.1.12b/perl/ |