calcTMTLFQPeptide: Calculates peptide data for individual TMT experiments

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

Calculates peptide data for individual TMT experiments

Description

For TMT and also for LFQ other than Mzion to flow through. Entries under the same pep_seq_mod at different z are collapsed.

Usage

calcTMTLFQPeptide(
  df = NULL,
  group_psm_by = "pep_seq",
  method_psm_pep = "median",
  group_pep_by = "prot_acc",
  dat_dir = NULL,
  set_idx = 1L,
  injn_idx = 1L,
  tmt_plex = 10L,
  rm_allna = FALSE,
  type_sd = "log2_R",
  engine = "mz"
)

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.
method_psm_pep	Depreciated. Character string; the method to summarize the log2FC and the intensity of PSMs by peptide entries. The log10-intensity of reporter ions at the PSMs levels will be the weight when summarizing log2FC with various "top_n" statistics or "weighted_mean". The choices of summary statistics for LFQ are depreciated at the users' levels.
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	Not used. An injection index.
tmt_plex	The multiplexity of TMT.
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.
engine	A search engine name.

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