Blog Archives

Stouffer’s meta-analysis with weight and direction effect in R

May 15, 2018
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I often have to perform meta-analysis of past experiments for which the only info I have is the fold change and the p-value (of any measure you may imagine: species richness, gene expression, depth of coverage, plates of carbonara eaten in 5 minutes, everything). The hardest thing to find out for me was how to

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Visualize KEGG pathway and fold enrichment

November 14, 2017
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Visualize KEGG pathway and fold enrichment

As a useful note to self, I paste here an easy example on the use of the pathview package by Weijun Luo to plot the log fold change of gene expression across a given KEGG pathway. This example is on Vitis vinifera (as the prefix vvi can suggest), but the approach is general. Basically, you

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Perform pairwise Wilcoxon test, classify groups by significance and plot results

March 25, 2017
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Perform pairwise Wilcoxon test, classify groups by significance and plot results

This post is the result of work performed in collaboration with my colleague Eleonora Paparelli (who actually did most of the work!). We wanted to compare several distributions using Wilcoxon test and summarize results (i.e. indicate the comparisons showing significant differences). R base includes pairwise.wilcox.test to perform Wilcoxon rank sum test between all pairs of

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Reading large data tables in R

May 2, 2014
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Reading large data tables in R

Ok, I confess. Until yesterday I was one of those still trying to read large data tables using read.table. Then, I came across this thread in stackoverflow and I saw the light. Since I noticed that a lot of people still struggle with read.table I decided to write this very brief post. Imagine that you

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Summarize content of a vector or data.frame every n entries

August 8, 2013
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Summarize content of a vector or data.frame every n entries

I imagine that the same result can be achieved by a proper use of quantile, but I like to have an easy way to obtain summary statistics every n entries of my dataset be it a vector or data.frame. The function takes three parameters: the R object on which we need to obtain statistics (x),

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R and theater

June 3, 2012
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R and theater

You might ask what R has to do with theater. I assure you it has. I act in the theater group ‘ndescenze. We will soon present (actually, we just performed) a show based on the Marx Brothers Radio Shows. We shuffle actors and characters during the show (we like it complicated!) and we needed to

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Introduction to R (Milano R course)

May 25, 2012
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Introduction to R (Milano R course)

I am happy to repost the information I got about the course “Introduction to R” that will be organized by Milano R net in collaboration with Quantide. The course will be held in Milano, Italy, June 7-8, 2012, and is intended to introduce the unexperienced user to R. For furhter info visit milano R net

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Milano R net meeting

April 24, 2012
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Milano R net meeting

I received the announce of the first Milano R net meeting, and I am glad to post it below. If you are based in Milano area you might think about going. If you are not based in Milano area, you might think about going as well! Milano R net Milano R net is a users

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Extract different characters between two strings of equal length

January 3, 2012
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Extract different characters between two strings of equal length

In the desperate effort of understanding the secret of life it may be too simplistic to just count the differences between two strings of equal length. You might as well want to know where they differ. You can do that recycling most of the function published in a previous post. You can use it to

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Count different positions between two strings of equal length

November 26, 2011
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Count different positions between two strings of equal length

This is another pretty simple function, written to help me solve the simplest representation of a trivial but tedious task. Most biologist are probably familiar with this task. How many nucleotide differences exist between two given sequences? I only faced the easiest part of the problem, i.e. I do not perform alignment, I just assume that

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