Maddocent

# Creating custom CDF for Affy chips in R / Bioconductor

```{r knitrOpts, echo=FALSE}
knit_hooks$set(inline = identity) # sets output for inline resutls nicely
knit_hooks$set(error = function(x, options) stop(x)) # kills knitr if there
# is an error, therefore we don't waste time generating error messages
options(save.defaults=list(compress="xz"), stringsAsFactors=FALSE) 
# set up the default compression, and do NOT allow strings in data frames to become factors.
# That one is really important, and continually messes me up.
startTime <- Sys.time() # when did we start

Maddocent

 
# Calculate age at a given reference date
# Create an interval between the date of birth and the enrollment date; 
# intervals are specific to the two dates. Periods give the actual length
# of time between those dates, so convert to period and extract the year.

calc_age <- function(birthDate, refDate = Sys.Date()) {

    require(lubridate)

Maddocent

#! /bin/sh

#####################################################################################################
#                                    == Thumbs_db_killer ==                                         #
# This script delete all the Thumbs.db files on the curent folder, and on the sub-folders.          #
# You can modify the $ennemy variable if you want to bulk-delete an other file (.Sync, of whatever).#
#   @author  : Tom Canac http://tomcanac.com/                                                       #
#   @version : 1.0                                                                                  #
#   @licence : CC-BY                                                                                #
#####################################################################################################

Maddocent

TL;DR

Include this in the .Rprofile in the top-level directory of an RStudio project:

RPROJ <- list(PROJHOME = normalizePath(getwd()))
attach(RPROJ)
rm(RPROJ)

Maddocent

% compile with
%   R CMD Sweave sweave_ggplot.Rnw
%   pdflatex sweave_ggplot.tex
\documentclass[t,ucs,12pt,xcolor=dvipsnames]{beamer}
\usepackage{fancyvrb}

\title{A sample Sweave demo}
\author{Author name}
\date{}

Maddocent

"%p%" <- function(left, right){
  paste(left, right)
}

Maddocent

# Here are a few methods for getting text from PDF files. Do read through 
# the instructions carefully! NOte that this code is written for Windows 7,
# slight adjustments may be needed for other OSs

# Tell R what folder contains your 1000s of PDFs
dest <- "G:/somehere/with/many/PDFs"

# make a vector of PDF file names
myfiles <- list.files(path = dest, pattern = "pdf",  full.names = TRUE)