Blog Archives

Downloading DNA sequences into R

August 15, 2010
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A while ago, a friend of mine needed to download a number of different DNA sequences from Genbank, the online repository for the vast majority of DNA sequences read from all organisms by labs all over the world. This is not a problem. The "ape" package in R has a nifty function, read.GenBank(), that downloads the...

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Transitions in R redux

April 28, 2010
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Previously, I shared with the world a function to create a pairwise matrix of the number of transitions and transversions between two DNA sequences. Klaus Schliep kindly pointed out the possibility of a bug in the function and offered a faster, more accurate version. Thanks Klaus! titv mat res for(i...

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Interrupting R processes in Ubuntu

March 16, 2010
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It's funny how things happen. Yesterday I was working away on a project in R and the unenjoyable happens---the process hangs for longer than desired. I operate R in the standard GNOME terminal in Ubuntu and the only way I knew was to close the entire a...

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Haplotype names in R

January 21, 2010
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Emmanuel Paradis, the mastermind behind 'ape' has struck again. This time he brings us the 'pegas' package, the Population and Evolutionary Genetic Analysis system. This package has a function that collapses the haplotypes (unique DNA sequences) in a DNA alignment, something which is extremely useful in various analyses and in the calculation of genetic diversity. library(ape)library(pegas)data(woodmouse)x h h...

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Earthquake maps

January 6, 2010
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Earthquake maps

There's been a number of earthquakes in the Solomon Islands over the past few days, including one that caused a tsunami to partially destroy the village of Baniata on Rendova, Western Provence. You can see exactly how many earthquakes have occurred the...

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Transitions and transversions in R

January 5, 2010
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Transitions and transversions in R

A couple of months ago I wrote the following R function to calculate the number of transitions and transversions between DNA sequences in an alignment. The function is fairly slow (an alignment of ~100 sequences, 800 bp in length takes around 30 second...

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Colour matching feature in R

December 8, 2009
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Colour matching feature in R

I love R. It is an open-source statistical programming language that I found reasonably easy to learn, and find it incredibly versatile and useful. Because it's open-source anyone can contribute to it, and there are a huge number of packages that exten...

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