In PeteHaitch/MethylationTuples: Tools for analysing methylation patterns at genomic tuples

BiocStyle::markdown()

Functions to write

Variable_naming.Scheme

Get some bloody consistency!

For submission to \Bioconductor{}

These are issues that must be addressed either before or during the \Bioconductor{} submission process.

Package name

I'm concerned the r Rpackage("MethylationTuples") name might be a bit long and clumsy.

I need to settle on a package name. r Rpackage("MethylationTuples") mimics the r Githubpkg("PeteHaitch/GenomicTuples") that it depends upon. It is also similar to \software{methtuple}, whose output files this package reads in and works with.

On a minor note: that \software{methtuple} is singular, whereas both r Githubpkg("PeteHaitch/GenomicTuples") and r Rpackage("MethylationTuples") are plural, grates on me.

Possible alternatives: r Rpackage("MethTuples"), other? Can't use r Rpackage("MethPat") as this is already being used.

Dependencies

The package will require BSgenome, but at this stage I'm not sure whether it should be in DEPENDS or IMPORTS. Various BSgenome-organism packages should be listed in SUGGESTS.

Questions

• [ ] How to document S4 methods/generics, in particular re @aliases?

PeteHaitch/MethylationTuples documentation built on May 8, 2019, 1:30 a.m.