Model scripts for R bioinformatics research

Question

[ddowlin]

Hi,

I am relatively new to bioinformatics/R/scripting. Currently I am trying to improve my coding style so that my scripts are more accessible, both for me and other readers.

Does anyone know of any resources for model scripts I could use as inspiration?

Thanks.

[EagleEye]

What do you mean by Model scripts? Are you looking for R tutorials?

[ddowlin]

What I mean is good examples of clean R code that is used in a bioinformatics context.

[Nicolas Rosewick]

http://stackoverflow.com/questions/420296/what-are-some-good-books-web-resources-and-projects-for-learning-r

[Medhat]

I Think you shall follow these

Google's R Style Guide
https://cran.r-project.org/web/packages/rockchalk/vignettes/Rstyle.pdf

Answer 1

[EagleEye]

This will be good starter for you,

https://cran.r-project.org/doc/contrib/Paradis-rdebuts_en.pdf (I have started with this PDF :-))

http://www.tutorialspoint.com/r/

Advanced usage of available pipelines:

For some high throughput analysis R scripts/packages look into Bioconductor website.

More discussions,

Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources

Answer 2

[Michael]

These are only a few coding style guides I found:

• https://www.bioconductor.org/developers/how-to/coding-style/
• http://r-pkgs.had.co.nz/style.html
• https://web.stanford.edu/class/cs109l/unrestricted/resources/google-style.html
• http://shape-of-code.coding-guidelines.com/2013/03/02/the-most-worthwhile-r-coding-guidelines-i-know/

If you want to look at examples from bioinformatics, you could take a look inside BioConductor packages, like BioStrings. But these are using advanced features of R's object system like methods, generics, etc. which might be overwhelming for a beginner.

Answer 3

[dariober]

Not related to bioinformatics, even less about R and not exactly concise... Still I'd recommend this book Code Complete. I found it very useful and readable.