join_mgfs: Joins MGF data to MSGF outputs.

In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data

Joins MGF data to MSGF outputs.

Description

Joins MGF data to MSGF outputs.

Usage

join_mgfs(
  dat_dir = NULL,
  mgf_path = NULL,
  mod_file = "MSGF_mods.txt",
  rm_reverses = FALSE,
  fdr_type = c("psm", "peptide"),
  target_fdr = 0.01,
  ...
)

Arguments

dat_dir	The working directory.
mgf_path	The path to MGF files. The default is file.path(dat_dir, "mgf").
mod_file	The name of the file specifying the MSGF+ modifications. The mod_file needs be under the dat_dir.
rm_reverses	A logical argument for uses with MaxQuant TMT and LFQ. At the TRUE default, Reverse entries will be removed.
fdr_type	The type of FDR control. The default is psm.
...	varargs; not currently used.
target_fder	A targeted false-discovery rate (FDR).

qzhang503/proteoQ documentation built on March 16, 2024, 5:27 a.m.