preMZpepLFQ: Pre-processing of Mzion PSM tables

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

Pre-processing of Mzion PSM tables

Description

Pre-processing of Mzion PSM tables

Usage

preMZpepLFQ(
  df = NULL,
  group_psm_by = "pep_seq_mod",
  group_pep_by = "prot_acc",
  dat_dir = NULL,
  set_idx = 1L,
  injn_idx = 1L,
  tmt_plex = 1L,
  rm_allna = FALSE
)

Arguments

df	A 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.
dat_dir	A working directory.
set_idx	A set index.
injn_idx	An injection index.
rm_allna	Logical; if TRUE, removes data rows that are exclusively NA across ratio columns of log2_R126 etc. The setting also applies to log2_R000 in LFQ.
TMT_plex	The multiplexity of TMT.

qzhang503/proteoQ documentation built on Feb. 27, 2025, 8:34 a.m.