Load PSMs from mzIdentML Files

This function loads Peptide-to-Spectrum Matches (PSMs) from mzIdentML files in a specified directory, combines them, and adds a standard column for the PSM score and protein reference.

Usage

iwf_load_psms(path = ".", pattern = ".mzid", psm_score = NULL, verbose = FALSE)

Arguments

path

A character string specifying the directory where the mzIdentML files are located. Default is the current working directory (".").

pattern

A character string representing the file pattern to search for. Default is ".mzid", which targets mzIdentML files.

psm_score

An optional character string specifying the column name to be used as the PSM score. If NULL, the last column in the loaded data will be used as the PSM score.

verbose

Logical, whether to print progress messages (default TRUE).

Value

A data.frame containing the combined PSM data, with added columns for the PSM score (psmScore) and the protein reference (proteinRef).