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Using R: writing a table with odd lines (again)

January 31, 2013
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Using R: writing a table with odd lines (again)

Let’s look at my gff track headers again. Why not do it with plyr instead? d_ply splits the data frame by the feature column and applies a nameless function that writes subsets to the file (and returns nothing, hence the ”_” in the name). This isn’t shorter or necessarily better, but it appeals to me.

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Using R: writing a table with odd lines (GFF track headers)

January 28, 2013
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Using R: writing a table with odd lines (GFF track headers)

The other day, I wanted to add track lines to a GFF file, so that I could view different features as separate custom tracks in a genome browser. The need to shuffle genome coordinates between different file formats seems to occur all the time when you deal with some kind of bioinformatic data. It’s usually

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A slightly different introduction to R, part II

January 27, 2013
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A slightly different introduction to R, part II

In part I, we looked at importing data into R and simple ways to manipulate data frames. Once we’ve gotten our data safely into R, the first thing we want to do is probably to make some plots. Below, we’ll make some simple plots of the made-up comb gnome data. If you want to play

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A slightly different introduction to R, part I

January 19, 2013
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A slightly different introduction to R, part I

Note in Swedish: Jag hoppas läsaren ursäktar att jag skriver på engelska då och då. This will be a brief introduction to using the statistics software R for biologists who want to do some of their data analysis in R. There are plenty of introductions to R (see here and here, for example; these are

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