psm_to_pep: Helper of PSM2Pep

psm_to_pepR Documentation

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",
  lfq_ret_tol = 60L,
  rm_allna = FALSE,
  type_sd = "log2_R",
  engine = "mz",
  lfq_mbr = FALSE,
  trace_files = NULL,
  ...
)

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

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.

lfq_ret_tol

The tolerance of retention time (in seconds) for the aggregation of LFQ data.

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.

lfq_mbr

Logical; performs MBR for LFQ or not.

...

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