In BrentLab/brentlabRnaSeqTools: Management/QC for brentlab RNAseq data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  echo = TRUE,
  include = TRUE,
  eval = FALSE
)

library(brentlabRnaSeqTools)

Using an Rstudio project

set your working directory

If you do not already have a directory in which you store the projects you work on, create one. I suggest a directory called projects in your $HOME

project_dir = "~/projects"
if(!dir.exists(project_dir)){
  dir.create(project_dir)
}
setwd(project_dir)

Set your global options

Next, in your Rstudio window, go to Tools -> Global Options. A window will open on the General tab. I recommend setting your default working directory to your new ~/projects directory. I also strongly recommend that you uncheck any box whose description starts with the word "Restore", make sure "Always save history" is unchecked, and if there is a dropdown option next to something that says "save worksapce to .RData", set that to never. You are probably going to be moving around a lot of data, and you don't want Rstudio trying to keep track of all of it. You're writing code -- if you do it somewhat carefully, it will always run and produce the same results. Save the code, don't save intermediate data, unless that intermediate data takes a long time to process. Note that you should also have an automatic backup set to backup your computer to a remote device, and I'd suggest also using github to track changes and as another backup for your code.

Creating a new Posit (Rstudio) project

A project is a subset of the infrastructure in an R software package. You can use a virtual environment, .Renviron files for environmental variables, etc. It is a tool for reproducibility

# if this is for the nineyMinuteInduction data, for example, you might call 
# this project "ninetyMinInduction".
project_name = "my_new_project"

usethis::create_project(project_name)

Using the project directory

A new Rstudio session will launch in your new project directory. Now, whenever you launch this project, all of your environment variables in .Renviron will be loaded. If you are using a virtual environment (a good idea for reproducibility. Use renv), then your virtual environment will be automatically launched, also.

The /R directory is for R scripts. You could make a notebooks directory, or just put the notebook in the project parent directory, for example.

See here for a project directory example

Using project level environmental variables in an active R project

Just as with the user level environmental variables (see the homepage), you can set environmental variables for a particular project. These are read in addition to the user level variables, and will overwrite them if there are two that are named the same thing. The first thing to do is to make sure that the project level .Renviron is in the .gitignore so that you don't accidentally push up login credentials to the cloud.

# you can use this, or just click on the .gitignore file in the project
usethis::edit_git_ignore('project')

In the .gitignore file, add .Renviron. Next, open a project level .Renviron

usethis::edit_r_environ("project")

and edit as before. Remember to re-launch your R session after editing the .Renviron to have access to the environmental variables.

BrentLab/brentlabRnaSeqTools documentation built on Aug. 20, 2023, 9:22 a.m.