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 a glyexp::expriment() object (from the glyexp package) for further analysis.

Installation

You can install the latest release of glyread from GitHub with:

# install.packages("pak")
pak::pak("glycoverse/glyread@*release")

Or install the development version:

pak::pak("glycoverse/glyread")

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 a glyexp::experiment() object 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"
)