pep_mf_lfq: Handling of MSFragger peptide table

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

Handling of MSFragger peptide table

Description

Fill back intensity values.

Usage

pep_mf_lfq(
  label_scheme,
  omit_single_lfq = FALSE,
  use_maxlfq = TRUE,
  group_psm_by = "pep_seq_mod",
  use_lowercase_aa = FALSE
)

Arguments

label_scheme	Experiment summary
use_maxlfq	Logical; use MaxLFQ values or not.
group_psm_by	A character string specifying the method in PSM grouping. At the pep_seq default, descriptive statistics will be calculated based on the same pep_seq groups. At the pep_seq_mod alternative, peptides with different variable modifications will be treated as different species and descriptive statistics will be calculated based on the same pep_seq_mod groups.
use_lowercase_aa	Logical; if TRUE, modifications in amino acid residues will be abbreviated with lower-case and/or ^_~. See the table below for details. The default is TRUE.

qzhang503/proteoQ documentation built on Dec. 14, 2024, 12:27 p.m.