Michael Grünstäudl (Gruenstaeudl), PhD

Postdoctoral Researcher at the Freie Universität Berlin

Monatsarchiv für August 2015

Generating automatic figure labels

Following the German motto “Ordnung ist das halbe Leben!” Have you ever been frustrated by having to differentiate between dozens of similar graphs or figures, and the only memorable difference between them were their unique file names? In a recent simulation study, I had exactly that feeling, so I came up with some code to […]

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State-matrix to presence-absence-matrix

A quick R example Today, I needed to convert a series of state matrices into presence-absence matrices. In order to automate this conversion, I wrote the following R code. (The initiated will recognize the output as a species-range matrix.) 1.a. Generate example input m = matrix(data=c(“A”,”B”,”C”), nrow=3, ncol=1) rownames(m) = c(“t1”, “t2”, “t3”) m [,1] […]

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Filtering out unpaired raw reads from Illumina data

Working at the intersection I have always wondered why an Illumina machine occasionally generates “unpaired” paired-end reads (i.e., when you receive an R1 but no corresponding R2, or vice versa). While I am waiting for a satisfactory answer, I would like to remove any unpaired reads from my data set in the meantime. Superficially, this […]

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