ogbox

A multi-purpose R package primarily for personal use

Installation

devtools::install_github('oganm/ogbox')

What’s in the box?

There are many poorly documented functions here. Below are some examples separated by category.

Developer tools

getVersion, setVersion and setDate functions allow manipulation of DESCRIPTION files. I use them for auto updating packages.

forkCRAN allows you to create a github repository for a current or older version of a cran package which can be followed up by install_github or Remotes in your DESCRIPTION file if you really need an older version of a package or want to make some changes yourself

List unpacking

Taken from this github answer ages ago, this syntax

list[a,b] = list(c(1,2,3),c(4,5,6))
a

## [1] 1 2 3

b

## [1] 4 5 6

allows unpacking of lists. These days zeallot package does that with %\<-% operator.

Remote code sourcing and data loading

• sourceGithub runs R scripts or specific lines of R scripts from github.
• loadURL and loadGithub loads remote rda files
• readRDSGithub reads an RDS file from github
• getGithubFile, also used by the functions above gets files from github.

Gene Expression Omnibus tools

Didn’t want to deal with S4 classes from bioconductor packages so there are a bunch of functions that deal with GEO datasets.

• gsmFind picks samples that match a regex from a dataset
• whichGSE finds the datasets that a sample belongs to
• gsmDown downloads cel files for microarray samples
• gseDown downloads all cel files for a microarray dataset
• softDown downloads softfile for an experiment
• softParser parses said soft file.