Getting Started with pepr

Nathan Sheffield

2020-10-16

Source: vignettes/gettingStarted.Rmd

Introduction to 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.

Installing 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')

Loading an example project

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')
## Registered S3 method overwritten by 'pryr':
##   method      from
##   print.bytes Rcpp
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)
## Loading config file: /private/var/folders/3f/0wj7rs2144l9zsgxd3jn5nxc0000gn/T/RtmpEYsaEm/temp_libpath43b174cbd72/pepr/extdata/example_peps-master/example_basic/project_config.yaml
## Warning in readLines(con): incomplete final line found on '/private/var/folders/
## 3f/0wj7rs2144l9zsgxd3jn5nxc0000gn/T/RtmpEYsaEm/temp_libpath43b174cbd72/pepr/
## extdata/example_peps-master/example_basic/project_config.yaml'

That’s it! You’ve now have a Project object, p, to interact with in R.

Interfacing with your pepr::Project object 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:

p
## PEP project object. Class:  Project
##   file:  
## /private/var/folders/3f/0wj7rs2144l9zsgxd3jn5nxc0000gn/T/RtmpEYsaEm/temp_libpath43b174cbd72/pepr/extdata/example_peps-master/example_basic/project_config.yaml
##   samples:  2

To get the sample table out of the project, you use the samples() function:

sampleTable(p)
##    sample_name      protocol                file
## 1:      frog_1 anySampleType data/frog1_data.txt
## 2:      frog_2 anySampleType data/frog2_data.txt

And you can also access the project configuration metadata with the config() function:

## Config object. Class: Config
##  pep_version: 2.0.0
##  sample_table: 
## /private/var/folders/3f/0wj7rs2144l9zsgxd3jn5nxc0000gn/T/RtmpEYsaEm/temp_libpath43b174cbd72/pepr/extdata/example_peps-master/example_basic/sample_table.csv
##  name: example_basic

Follow the other vignettes for more advanced capabilities of pepr.