psm_to_pep: Helper of PSM2Pep

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

Helper of PSM2Pep

Description

Helper of PSM2Pep

Usage

psm_to_pep(
  file = NULL,
  df = NULL,
  dat_dir = NULL,
  label_scheme_full = NULL,
  group_psm_by = "pep_seq",
  group_pep_by = "prot_acc",
  method_psm_pep = "median",
  rm_allna = FALSE,
  type_sd = "log2_R",
  engine = "mz",
  use_spec_counts = FALSE,
  ...
)

Arguments

file	The name of a PSM file.
df	A PSM table.
dat_dir	A character string to the working directory. The default is to match the value under the global environment.
label_scheme_full	The label_scheme with the probable inclusion of different LCMS_inj under the same TMT_Set.
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.
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.
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	The search engine name.
use_spec_counts	Logical; use spectrum counts or not.
...	filter_dots.
ok_lfq	Logical; performs LFQ or not.

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