Read MSFragger-Glyco result

MSFragger-Glyco is a software for glycopeptide identification and quantification. This function reads in the result file and returns a glyexp::experiment() object.

Usage

read_msfragger(
  dp,
  sample_info = NULL,
  quant_method = "label-free",
  glycan_type = "N",
  sample_name_converter = NULL
)

Arguments

dp

The directory path of the MSFragger-Glyco result folder.

sample_info

File path of the sample information file (csv), or a sample information data.frame/tibble.

quant_method

Quantification method. Either "label-free" or "TMT".

glycan_type

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

sample_name_converter

A function to convert sample names from file paths. The function should take a character vector of old sample names and return new sample names. Note that sample names in sample_info should match the new names. If NULL, original names are kept.

Value

An glyexp::experiment() object.

Details

This function uses the "psm.tsv" file in each sample folder. Sample names are extracted from the file paths. They are the parent of each "psm.tsv" file. For example, "msfragger_result/H1/psm.tsv" will be named "H1".

Variable information

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

• peptide: character, peptide sequence

• peptide_site: integer, site of glycosylation on peptide

• protein: character, protein accession

• protein_site: integer, site of glycosylation on protein

• gene: character, gene name (symbol)

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

See also

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