R programming language

Introduction to cowplot to combine several plots in one with R

Hi everyone, Today I will introduce cowplot, an extension of ggplot2 library. Some helpful extensions and modifications to the 'ggplot2' package. In particular, this package makes it easy to combine multiple 'ggplot2' plots into one and label them with letters, e.g. A, B, C, etc., as is often required for scientific publications. As you can see, this library can be useful to easily create a figure containing multiple plots. But we will see how we can use it to create [...]

By | November 28, 2016|Categories: Bioinformatics, Biology, Data Analysis, Data Visualisation, R|0 Comments

Pivoting tables : from long to wide

As bioinformaticians, we often have to work with data that are not formatted the way we would need them to be. One case we might encounter is receiving data in a "long" format instead of receiving them in a more familiar "wide" format. For those of you familiar with the ggplot R package, you know this format very well. It's the format required by ggplot to produce its nice graphs. Long genes samples expression 1 BAD S01 7.525395 2 BAD [...]

By | November 14, 2016|Categories: Python, R|0 Comments

Bootstraps and Confidence Intervals

When analyzing data, you might want or need to fit a specific curve to a particular dataset. This type of analysis can result in instructive outputs regarding the relationship between two (or more...) quantifiable parameters. The main object of this post is not how to implement such fitting, but rather how to display the goodness of such a fit i.e. how to calculate a confidence interval around a fitted curve. That being said, I will show how to do curve fitting in [...]

By | September 29, 2016|Categories: Data Analysis, Data Visualization, R|1 Comment

Simple multiprocessing in R (2nd edition)

The last time I spoke about this subject, I presented a really simple way to change an lapply call into its multicore sibling mclapply. Now while this is an extremely easy modification to implement in your code to gain substantial performance benefits, it kinda required you to be making use of the lapply function in the first place. So let's look at another way to introduce multiprocessing into your existing codebase with the use of the foreach and doMC packages. [...]

By | September 19, 2016|Categories: Performance, R|0 Comments

Fastest method to compute an AUC

Context: AUC is an acronym for "Area Under the (ROC) Curve". If you are not familiar with the ROC curve and AUC, I suggest reading this blog post before to continuing further. For several projects, I needed to compute a large number of AUC. It started with 25,000, increased to 230,000 and now I need to compute 1,500,000 AUC. With so many AUC, the time to compute each one becomes critical. On the web, I don't find much information about this specific [...]

By | August 18, 2016|Categories: Data Analysis, Performance, Python, R, Statistics|0 Comments