glyread

The goal of glyread is to read and process quantification results from common glycomics and glycoproteomics software, such as Byonic, StrucGP, or pGlyco, and convert them into glyexp::GlycomicSE or glyexp::GlycoproteomicSE objects (from the glyexp package) for further analysis.

Installation

Install glycoverse

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

Install glyread alone

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

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

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

Or from GitHub:

Install the latest releases of this package and its required Glycoverse dependencies together from GitHub:

pak::pkg_install(c(
  "glycoverse/glyrepr@*release",
  "glycoverse/glyexp@*release",
  "glycoverse/glyparse@*release",
  "glycoverse/glyread@*release"
))

Or install the development version (NOT recommended):

pak::pkg_install("glycoverse/glyread")

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

Documentation

• Getting started: Here
• Reference: Here

Role in glycoverse

glyread is the entry point for the glycoverse ecosystem. It provides a unified interface for reading and processing data from various glycomics and glycoproteomics software, and converting them into glyexp::GlycomicSE or glyexp::GlycoproteomicSE objects for further analysis.

Example

Used pGlyco3 and pGlycoQuant for glycopeptide identification and quantification? Try read_pglyco3_pglycoquant()!

library(glyread)

exp <- read_pglyco3_pglycoquant(
  "path/to/pGlyco3-pGlycoQuant/result/Quant.spectra.list",
  sample_info = "path/to/sample_info.csv",
  quant_method = "label-free",
  glycan_type = "N"
)