tidy_fragpipe_psm – prolfquapp

read psm.tsv produced by FragPipe and convert into long format

Description

read psm.tsv produced by FragPipe and convert into long format

Usage

tidy_FragPipe_psm(
  psm_files,
  purity_threshold = 0.5,
  PeptideProphetProb = 0.9,
  abundance_threshold = 0,
  column_before_quants = c("Quan Usage", "Mapped Proteins"),
  aggregate = TRUE
)

Arguments

psm_files path(s) to psm.tsv file(s)

purity_threshold purity threshold default = 0.5

PeptideProphetProb default 0.9

abundance_threshold minimum abundance threshold

column_before_quants describes the last column before the quantitative values (not consistent across FP versions), default "Quan Usage"

aggregate aggregate spectra to psm level

Value

A list with the long-format PSM data and expected peptide counts.