pepr
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 yaml
file. 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.
pepr
You can install pepr
in the usual way. Currently from GitHub (but we target a CRAN release at some point).
devtools::install_github('pepkit/pepr')
Load 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 yaml
file:
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 R
.
pepr::Project
object in RNow 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:
p
To get the sample table out of the project, you use the samples()
function:
sampleTable(p)
And you can also access the project configuration metadata with the config()
function:
config(p)
Follow the other vignettes for more advanced capabilities of pepr
.
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