Skip to contents

Read the result from StrucGP

read_strucgp.Rd

StrucGP is a software for intact glycopeptide identification. As StrucGP doesn't support quantification, this function returns an glyexp::experiment() object with a binary (0/1) expression matrix indicating whether each glycopeptide was identified in each sample.

Usage

read_strucgp(fp, sample_info = NULL, glycan_type = "N", parse_structure = TRUE)

Arguments

fp

File path of the StrucGP result file.

sample_info

File path of the sample information file (csv), or a sample information data.frame/tibble. If NULL (default), a simple sample information tibble will be created.

glycan_type

Glycan type. Either "N" or "O". Default is "N".

parse_structure

Logical. Whether to parse glycan structures. If TRUE (default), glycan structures are parsed and included in the var_info as glycan_structure column. If FALSE, structure parsing is skipped and the structure column is removed.

Value

An glyexp::experiment() object with a binary (0/1) expression matrix, where 1 indicates the glycopeptide was identified in that sample and 0 indicates it was not.

Variable information

The following columns could be found in the variable information tibble:

  • peptide: character, peptide sequence

  • protein: character, protein accession

  • gene: character, gene name (symbol)

  • protein_site: integer, site of glycosylation on protein

  • glycan_composition: glyrepr::glycan_composition(), glycan compositions.

  • glycan_structure: glyrepr::glycan_structure(), glycan structures (if parse_structure = TRUE).

Sample information

The sample information file should be a csv file with the first column named sample, and the rest of the columns being sample information. The sample column must match the file_name column in the StrucGP result file, although the order can be different.

You can put any useful information in the sample information file. Recommended columns are:

  • group: grouping or conditions, e.g. "control" or "tumor", required for most downstream analyses

  • batch: batch information, required for batch effect correction

See also

glyexp::experiment(), glyrepr::glycan_composition(), glyrepr::glycan_structure()