Blog Archives

Joining data frames in R

December 17, 2009
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Joining data frames in R

Want to join two R data frames on a common key? Here's one way do a SQL database style join operation in R.We start with a data frame describing probes on a microarray. The key is the probe_id and the rest of the information describes the location on t...

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Using R and Bioconductor for sequence analysis

August 26, 2009
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Using R and Bioconductor for sequence analysis

Here's another quick R vignette, in case I pick this up later and need to remind myself where I got stuck. I was trying to use R for a bit of basic sequence analysis, with mixed results.First, install the BSgenome package, which is part of Bioconductor...

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Select operations on R data frames

July 26, 2009
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Select operations on R data frames

The R language is weird - particularly for those coming from a typical programmer's background, which likely includes OO languages in the curly-brace family and relational databases using SQL. A key data structure in R, the data.frame, is used somethin...

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Parsing GEO SOFT files with Python and Sqlite

July 17, 2009
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Parsing GEO SOFT files with Python and Sqlite

NCBI's GEO database of gene expression data is a great resource, but its records are very open ended. This lack of rigidity was perhaps necessary to accommodate the variety of measurement technologies, but makes getting data out a little tricky. But, a...

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R String processing

July 2, 2009
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R String processing

Here's a little vignette of data munging using the regular expression facilities of R (aka the R-project for statistical computing). Let's say I have a vector of strings that looks like this:> coords "chromosome+:157470-158370" "chromosome+:1583...

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How to plot a graph in R

June 2, 2009
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How to plot a graph in R

Here's a quick tutorial on how to get a nice looking graph out of R (aka the R Project for Statistical Computing). Don't forget that help for any R command can be displayed by typing the question mark followed by the command. For example, to see help o...

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Results of the St. Pat’s 10 Miler and 5K

March 23, 2008
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Results of the St. Pat’s 10 Miler and 5K

Recently I ran the St. Pat’s 10 Miler in Atlantic City, Nj. It was my first official running event ever and I enjoyed it lot. Shortly after the race the official results have been posted on the Internet. The data did not only include the number and times of the participants but also gender and … Continue reading...

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