Dear list, I am try to write some long R script. Does anyone can recommend some good examples on Bioconductor to read its source code? So I can learn how to write long R script more quickly in R's way. Thank you very much in advance.

Hi Fabrice, Rather than writing a single long script, may I suggest you try to modularize your code? In other words, it is easier to write, test, and maintain multiple functions, each of which does a single thing, rather than one monolithic piece of code. When writing my own code I try to follow two principles; keep each function under a page in length, and if I am doing the same (relative) thing twice or more, strip that code out and put it in its own function. Of course these aren't hard rules, and I do have some really long spaghetti code in my code base, so there you are. There are many BioC packages that follow this paradigm, including pretty much all the packages that are supplied by the core authors. The biggest drawback to this type of coding is that it is difficult for those not familiar with the code base to figure out what is going on. Compare for example the code for heatmap.2 in gplots, which is one great hunk of spaghetti code to something like the table creation functions in table.R of annaffy (https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/annaffy/R /table.R). Those two examples are extremes. There are almost 400 lines in heatmap.2() whereas each of the table functions in annaffy are maybe 50 lines, max. Best, Jim On 5/15/2012 10:09 PM, Fabrice Tourre wrote: > Dear list, > > I am try to write some long R script. Does anyone can recommend some > good examples on Bioconductor to read its source code? > > So I can learn how to write long R script more quickly in R's way. > > Thank you very much in advance. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099