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Recent articles

February 28, 2014 Leave a comment

Just a small review of the articles I went through recently :

  • A surprising results on sex bias in Holstein. Huge impact on the industry could be thought of, if the figure are confirmed and impact better estimated (I mean, conventional semen give 50% of females. So the worst case scenario against which +450 kg more milk at the end of the second lactation could be produced…is not the common situation).
  • Analysis of selective sweep in cattle with sequence data.
  • Some hints on way to correct for population stratification
  • The funny article of the month, a compression exercise with all the results included (Side effect of the OpenData policy ? …lots of information you’ll never really use ?)

Recent articles

January 21, 2014 Leave a comment

Just a small review of the articles I went through recently :

Recent articles

October 31, 2013 Leave a comment

Just a small review of the articles I went through recently :

Recent articles

August 1, 2013 Leave a comment

Just a small review of the articles I went through recently :

  • Why proper definition of any statistic matter. An article on the numerous Fst definitions, and their respective behavior with varying assumptions : MAF spectrum, samples size etc.  The article is very comprehensive and give a nice review of main concept around Fst.
  • Still around population genetics an article of my PhD supervisor on selective sweeps identification. The supporting information are also pretty worthy.
  • A nice review on measure of dependence it’s a  real relief to see alternative to the correlation coefficient do exist ! I must admit that pointless statements like “X and Y are correlated at 5%” just kill me.
  • “Encode returns” a reply to Graur’s article by Mattick and Dinger.
  • While at first glance its title may sound rather tautological, this article on long intergenic non coding RNA nicely shows that similar behavior (Ribosome occupancy) does not imply similar results (Protein coding). I wondered if the absence of stop codon in lincRNA (and thus the absence of ribosome release) impact the cell, but apparently lincRNA are not numerous enough to have any substantial effect.

Serial snapshots with IGV batch

July 16, 2013 Leave a comment

IGV is a very handy tool. Nevertheless, scrolling from one position to another may be fastidious. Second, the bad aspect of this very user-friendly software, is that you can spend hours looking here and there, with at last no backtrack of your discoveries.

Thankfully, IGV can run in batch mode, allowing, for a targeted list of positions, to take screenshots and store the later in a folder. We’ll illustrate in the following with a small example :

Setting up a session

To test our script, we will first download some publicly available data.

#Download a vcf file (on beagle4 website, you may have to change file name according to last release)
wget http://faculty.washington.edu/browning/beagle/test.r1099.vcf.gz
gunzip test.r1099.vcf.gz
#Create an index
igvtools index test.r1099.vcf
#(You can alternatively prefer to use igvtools from igv GUI)
#Launch igv
igv.sh

To check if everything is right, load the vcf file test.r1099.vcf. Then move to positions chr22:20,000,000-20,100,000.

IGV

Set everything to your taste, and save the session :  File, save session, you should obtain a xml file.

Running IGV in batch mode

Now, let’s consider you are interested in some particular position. Let’s say we’ve stored several positions of interest in a csv file. Our aim is to create an IGV batch file.

Basically, we’ll have to load the session, set a directory to store the screenshots, and then move from one position to the other. A very crude version could therefore be. (I know : Why csv ? Because a lot of person still use excel 😦 )

#Create a fake positions list
cat >Liste.csv <<EOF
chr22;20070000
chr22;20081000
EOF

#Create a ss directory
mkdir IMG
#Write the header of the script
cat >Batch.igv <<EOF
new
load igv_session.xml
snapshotDirectory IMG
EOF
#Now parse the csv file
gawk -F ";" -v R=10000 '{print "goto "$1":"$2 -R"-"$2 + R"\nsnapshot Screen"NR".png"}END{print "exit"}' Liste.csv >>Batch.igv

From, igv, go to Tools, Run a batch script. Load Batch.igv, when all the process will be done, IGV will terminate and you’ll find your screenshots in IMG.

For an even more automated version you can use the script “PrepIgvBatch.sh” available in the scriptotheque

Recent articles

July 8, 2013 Leave a comment

Just a small review of the articles I went through recently :

Sufficiently rare to be mentioned, Bayes theorem in Science  by  Efron , with a nice follow-up post on the og

Although the lab technicalities were far beyond my understanding, the questions raised by this article on Evolution of  essential gene, stroke me !

I wish I had time to have a look on these kind of procedure during my  Ph’D, a simple permutation algorithm to compute significance threshold. By the way, I also learned a new distribution : the Rademacher distribution

I was eager to see this article, the Rat Genome Sequencing and Mapping consortium  made a very interesting piece of work combining sequence and genetic mapping in outbred rats. A lot of questions came to my mind based on these results…yeah hunting the so called “causal mutation” may not be that easy.

And last the funny  article of the month ! This kind of question could have been seen on  Freakonometrics

Beamer theme creation

June 13, 2013 1 comment

inrabeamerAs mentioned in a previous post , INRA renewed it’s visual identity. Unfortunately no beamer theme was provided. This gave me the occasion to look a bit deeper on beamer’s theme and how to create a relatively simple INRA theme.

I tried to keep things simple. Thus, I first identify the main characteristics of the powerpoint template.

  1. First slide have a green background while others slides have a white background and a logo on the left of the header
  2. General colors for title and subtitle are two specific green (with a precise RGB code)
  3. All the slides contains author name, presentation title, and date in their footer.

Beamer theme are defined through “.sty” files. Here, we’ll create a file named beamerthemeINRA.sty , the later will be used via the command \usetheme{INRA} in our source code. The beamerthemeINRA.sty itself, contain instructions to include sty files each defining a part of the theme.

\ProvidesPackage{beamerthemeINRA}[]
\useoutertheme{INRA}

We will address the solutions I’ve adopted for each of the 3 main points of the INRA theme.

Background

The Background can be changed in the outtertheme, we have to redefine the canvas template and include a background image.

In my case, to get the background, I opened the powerpoint templates, removed any text made  screen-shots of it. The screen-shots were then pasted in gimp, and saved as png. Now, in the file outerthemeINRA.sty we define the images to include in the background. As we’ll use a different background on the first slide, we’ll need a conditional instructions.

\setbeamertemplate{background canvas}{%
 \ifnum\c@framenumber=1%First slide
 \includegraphics[width=\paperwidth,height=\paperheight]{bgINRA1}
 \else%Other slides
 \includegraphics[width=\paperwidth,height=\paperheight]{bgINRA2}
 \fi%
 }

First test, add \usetheme{INRA} in your source code, check bgINRA1 and bgINRA2, and all the sty file are in the current directory. Compile, check your pdf (things should already be pretty close to what you expect).

The title slide is obviously not where it should it should ! We’ll have to tweak the title template. After a quick look at some other beamer theme, and series of trials and errors, I  end out with this bunch of code :

Colors

Colors are generally defined in a beamercolortheme.sty file.

\definecolor{INRA@lgreen}{RGB}{188,214,49}
\definecolor{INRA@dgreen}{RGB}{139,172,33}
\setbeamercolor{structure}{fg=INRA@dinst}

Structure will define the color set for most of the elements of your presentation. We define only the foreground color, since a background colour would hide the upper left logo in the background. Now add \usecolortheme{INRA} to the beamerthemeINRA.sty, compile and check the results.

Footline

Back to the outertheme, we now want to add the author, presentation title and date in the footline. Once again, after a look at other theme, we copy paste code that look close to what we are looking for. Proceed by trial and errors, until obtaining a satisfactory result. For me it gave something like :

%footline
 \defbeamertemplate*{footline}{INRA theme}{
 \begin{beamercolorbox}[wd=\paperwidth,ht=15 pt,leftskip=1.5cm,dp=1ex]{structure.fg}%
 \color{white}\qquad \insertauthor\qquad\color{INRA@linst}\inserttitle \hfill \color{white}\insertdate\par
 \end{beamercolorbox}
 }

Useful resources

The theme is now available on the animal genetics’ forge

In order to create the theme, I googled a lot, here is a stack of useful link I went trough, it might be of interest to you.

http://www.tug.org/pracjourn/2005-4/mertz/mertz.pdf

http://en.wikibooks.org/wiki/LaTeX/Presentations

http://mcclinews.free.fr/latex/beamermodif.php

http://www.math.umbc.edu/~rouben/beamer/quickstart.html

http://distrib-coffee.ipsl.jussieu.fr/pub/mirrors/ctan/macros/latex/contrib/beamer/doc/beameruserguide.pdf

http://programming-r-pro-bro.blogspot.fr/2011/11/create-your-own-beamer-template.html

Categories: Communication, LaTeX