Emir Turkes eturkes

The knitr themes manual can be found at (Rnw source).

	## RNA-seq analysis with DESeq2
	## Stephen Turner, @genetics_blog

	# RNA-seq data from GSE52202
	# http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse52202. All patients with
	# ALS, 4 with C9 expansion ("exp"), 4 controls without expansion ("ctl")

	# Import & pre-process ----------------------------------------------------

	# Import data from featureCounts

	#' Simplified loading and installing of packages
	#'
	#' This is a wrapper to \code{\link{require}} and \code{\link{install.packages}}.
	#' Specifically, this will first try to load the package(s) and if not found
	#' it will install then load the packages. Additionally, if the
	#' \code{update=TRUE} parameter is specified it will check the currently
	#' installed package version with what is available on CRAN (or mirror) and
	#' install the newer version.
	#'
	#' @param pkgs a character vector with the names of the packages to load.

	#!/bin/bash

	# $1: PID
	# Returns true if a process exists with pid=PID
	function isProcessAlive {
	if [ `ps -p $1 \| wc -l` -gt 1 ] ; then
	return 0;
	else
	return 1;
	fi

	n = 100 # No. of samples per treatment
	mean.A = 10 # Mean count for treatment A
	mean.B = 5 # Mean count for treatment B
	nd = data.frame(Trt = c("A", "B")) # Used in predict( ) function

	# Generate example data based on Poisson distribution (mean = variance)
	data.pois = data.frame(Trt = c(rep("A", n), rep("B", n)),
	Response = c(rpois(n, mean.A), rpois(n, mean.B))
	)