pepr is the official R package for the pepkit suite, a collection of tools that interface with portable encapsulated projects, or PEPs. PEP format defines a structure for organizing project metadata using a
pepr allows you to read any PEP-formatted project metadata (and potentially even actual sample data) into R, providing you a convenient user interface to interact with and share project metadata.
You can install
pepr in the usual way. Currently from GitHub (but we target a CRAN release at some point).
pepr and read in your project. We have provided a basic example to show you how it works. You can use this to get the file path to a built-in example project configuration
library('pepr') branch = "master" projectConfigFile = system.file("extdata", paste0("example_peps-", branch), "example_basic", "project_config.yaml", package="pepr")
Loading your project metadata into R is a single line of code:
p = pepr::Project(file=projectConfigFile)
That's it! You've now have a
Project object, p, to interact with in
pepr::Projectobject in R
Now you can interface with that project object to grab both sample-level and project-level metadata. Here's how you can access the metadata. If you just run the
show() function on your object, you'll get a simple report telling you a few basic stats, like where the project came from and how many samples it has:
To get the sample table out of the project, you use the
And you can also access the project configuration metadata with the
Follow the other vignettes for more advanced capabilities of
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