assign_duppeps: Assign duplicated peptides to a leading protein

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

Assign duplicated peptides to a leading protein

Description

Assign duplicated peptides to a leading protein

Usage

assign_duppeps(
  df,
  group_psm_by = "pep_seq",
  group_pep_by = "pep_seq_mod",
  use_duppeps = TRUE,
  duppeps_repair = "denovo"
)

Arguments

df	A PSM data frame
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.
group_pep_by	A character string specifying the method in peptide grouping. At the prot_acc default, descriptive statistics will be calculated based on the same prot_acc groups. At the gene alternative, proteins with the same gene name but different accession numbers will be treated as one group.
use_duppeps	Logical; if TRUE, re-assigns double/multiple dipping peptide sequences to the most likely proteins by majority votes.
duppeps_repair	Not currently used (or only with majority). Character string; the method of reparing double-dipping peptide sequences upon data pooling. For instance, the same sequence of PEPTIDE may be assigned to protein accession PROT_ACC1 in data set 1 and PROT_ACC2 in data set 2. At the denovo default, the peptide to protein association will be re-established freshly. At the majority alternative, a majority rule will be applied for the re-assignments.

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