calcLFQPeptide: Calculates Mzion peptide data for individual samples

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

Calculates Mzion peptide data for individual samples

Description

Argument injn_idx does not currently used.

Usage

calcLFQPeptide(
  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,
  ok_lfq = TRUE,
  rm_allna = FALSE,
  type_sd = "log2_R"
)

Arguments

df	A data frame.
dat_dir	A working directory.
set_idx	A set index.
injn_idx	Not used. An injection index.
tmt_plex	The multiplexity of TMT.
ok_lfq	Logical; performs LFQ or not.
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.
type_sd	Character string; the type of log2Ratios for SD calculations. The value is one log2_R, N_log2_R or Z_log2_R.

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