psmtsv_to_modified_peptides: Process 'psm.tsv' file into modified peptides

In MiguelCos/fragNterminomics: Annotation and processing of peptides from FragPipe search results

Process 'psm.tsv' file into modified peptides

Description

Filters the ‘psm.tsv' based on a ’best PSM' criteria; based on purity and summed TMT reporter intensities. Zero (0) abundance values are substituted by NA (missing values).

Usage

psmtsv_to_modified_peptides(psms, annot, peptide_probability, minimal_purity)

Arguments

psms	Data frame obtained from loading the 'psm.tsv' file from Fragpipe output
annot	Data frame obtained from loading the 'annotation.txt' from Fragpipe output. First column should be named 'channel' and second column should be named 'sample'.
peptide_probability	Minimal peptide probability accepted per PSM
minimal_purity	Minimal isobaric purity accepted per PSM

Value

Data frame of summarized modified peptides based on their 'best PSMs' based on the filtering criteria

MiguelCos/fragNterminomics documentation built on Oct. 13, 2023, 5:31 a.m.