Publications by fabiomarroni
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 blog. Related To leave a comment f...
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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 find at least one sequence of scenes which allowed ...
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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), how many entries should each summary contain (step, default...
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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 have your large file named “mylargefile.txt...
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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 Wil...
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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 just need to feed pathview the pathway argument and a gen...
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Stouffer’s meta-analysis with weight and direction effect in R
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 take the direction of the changes in...
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Use R to write multiple tables to a single Excel file
The possibility of saving several tables in a single file is a nice feature of Excel. When sharing results with colleagues, it might be useful to compact everything in a single file. As a bioinformatician, I am too lazy to do that manually, and I searched the web for tools that allow doing that. I found out that there are at least two R packages ...
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Nice tables in R
I used to think that making nice table in R is not worth the effort. However, after changing my mind for the billionth time on relatively large tables for a paper and do not wanting to reformat them again from scratch, I gave a try to the formattable package, and I liked it very much. I post here some basic formats I learnt from the web. Note: I ...
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