Statistical Analysis of Glycoproteomics and Glycomics Data • glystats

The goal of glystats is to perform statistical analysis on glycoproteomics and glycomics data. It works seamlessly with the glyexp package.

Installation

Install glycoverse

We recommend installing the meta-package glycoverse, which includes this package and other core glycoverse packages.

Install glystats alone

If you don’t want to install all glycoverse packages, you can only install glystats.

You can install the latest release of glystats from r-universe (recommended):

# install.packages("pak")
pak::repo_add(glycoverse = "https://glycoverse.r-universe.dev")
pak::pkg_install("glystats")

Or from GitHub:

pak::pkg_install("glycoverse/glystats@*release")

Or install the development version (NOT recommended):

pak::pkg_install("glycoverse/glystats")

Note: Tips and troubleshooting for the meta-package glycoverse are also applicable here: Installation of glycoverse.

Documentation

🚀 Get started: Here
📚 Reference: Here

Role in `glycoverse`

glystats is the downstream analysis package in the glycoverse ecosystem. It provides statistical analysis functions for glyexp::experiment() objects. A common workflow is to use glyread to import data, glyclean to preprocess data, and then glystats to perform statistical analysis.

Example

Say we already have a preprocessed experiment object called exp:

# Two-sample t-test
ttest_res <- gly_ttest(exp)

# PCA analysis
pca_res <- gly_pca(exp)

# ROC analysis
roc_res <- gly_roc(exp)

That’s it! These functions use glycoverse column conventions to load needed data and perform analysis. All functions start with gly_ to leverage the auto-completion in RStudio. They accept an glyexp::experiment() object, and return analysis result as a tibble or a list of tibbles. See documentation for each function for more details.

glystats