Next steps

We have barely touched the surface of what R has to offer today. If you want to take your skills to the next level, here are some topics to investigate:

Programming

• Writing functions.
• Using if statements.

The Software Carpentry in R course introduces R as a programming language.

Tidying and summarizing data

• dplyr by Hadley Wickham, and also tidyr, readr, stringr.
• magrittr’s %>% operator for chaining together data frame manipulations.

These tools play well with ggplot2, which we saw in the previous chapter.

Bioinformatics

Bioconductor is a collection of bioinformatics related packages, including the popular limma and edgeR packages for RNA-Seq analysis developed at the Walter and Eliza Hall Institute, and packages such as rtracklayer, GenomicRanges, and Biostrings for working with DNA/RNA/protein sequences and genomic features.

• Bioconductor cheat sheet

Even more functions and packages

• RStudio’s collection of cheat sheets cover newer packages in R.
• An old-school cheat sheet for dinosaurs and people wishing to go deeper.
• CRAN has hundreds of contributed packages which can be installed with install.packages.

As ever, the help system ?functionname is your friend.

Statistics

• Many statistical tests are built in to R.

• Linear models, and the linear model formula syntax ~, are core to much of what R has to offer statistically.
  • Many statistical techniques take linear models as their starting point, including limma which we will be using to test for differential gene expression.
  • Many R function repurpose the ~ formula syntax for other ways of relating response and explanatory variables.

See “The R Book” by Michael J. Crawley for general reference.

The books “Linear Models with R” and “Extending the Linear Model with R” by Julian J. Faraway cover linear models, with many practical examples.

Q&A sites

Stackoverflow-style sites are great for getting help:

• support.bioconductor.org for bioconductor related questions.
• biostars.org for general bioinformatics questions.
• stats.stackexchange.com for statistics questions.
• stackoverflow.com for general programming questions.

Community

The Monash Bioinformatics Platform offers:

• Weekly drop in sessions where you can get help with R, or general bioinformatics problems.
• Informal Wednesday afternoon talks, which often relate to R.
• Courses on various topics through the year.

Join the mailing list to hear about future events.

Also, the COMBINE student and early career researcher organization runs Software Carpentry workshops.