README.md

In LittleHeronCodes/Lazy2: Lazy Package

Lazy2

Custom functions from Lazy for personal use, now as a package!

Version 0.2.0 To Do

• [ ] Functions : plotMA, plotVol -- turn into one function with option. (Deprecate plotVol)
• [x] Functions : change the variable oddsRatio to FE as Fold enrichment is the more accurate term.
• [ ] Functions : ent2sym -- better type checking
• [ ] Functions : extractGeneList : p value column into option. (Also check if column actually exists)
• [ ] Issues : Pathway analysis gene space problem. Need to update gene space after removing pathways less than minimum gene space.
• [ ] Functions : ens2sym
• [ ] Datasets : Add mouse gene info
• [ ] Datasets : Update LazygeneInfo

Checklist before moving to 0.2.0

Ver 0.2.0 is final backward incompatible change.

• [x] Test all functions vigorously.
• [x] All functions used frequently in last two projects.
• [x] Descriptions in all functions.
• [x] Read last reference article on releasing R package.
• [x] Read up on gitFlow.

Version 0.2 Ideas

~- [ ] Think about utilizing cpp codes for simple calculation function. --> speed trade-off potentially not worth it~ - [ ] Mathematical equations into help page. (if possible)

Note to Self

• Be sure to run DATASET.R when adding new data.
• Package must be rebuilt to update manuals.
• Test build on local before deployment.
• Reduce dependency.

Version Numbers

major.minor.patch.dev

• minor : function add, modify, new builds (manual updates)
• patch : minor bug fix, function tweaks
• dev : 9000. Indicating in development.

Testing Build

getwd() #'path/to/alt/RLib/Lazy2'
library(devtools)
build()
document()
check()

Installation Guide

.libPaths('path/to/alt/RLib')
devtools::install_github('LittleHeronCodes/Lazy2')
library(Lazy2, lib.loc = 'path/to/alt/RLib')

Update Guide

library(roxygen2)
library(devtools)

getwd()
#'path/to/alt/RLib/Lazy2'
document()
build()
install()

# reload package
reload(inst('Lazy2'))

Useful Links and References

• R Namespaces
• Package structure by CRAN
• Writing R Packages by Karl Broman
• Releasing a package
• A successful Git branching model
• Exploring Package Startup messages

LittleHeronCodes/Lazy2 documentation built on Jan. 26, 2024, 2:01 p.m.