calc_sd_fcts_psm: Calculates PSM SDs

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

Calculates PSM SDs

Description

The standard deviations are based on samples under each TMT set and LCMS.

Usage

calc_sd_fcts_psm(
  df,
  range_log2r = c(5, 95),
  range_int = c(5, 95),
  set_idx,
  injn_idx
)

Arguments

df	The name of a primary data file. By default, it will be determined automatically after matching the types of data and analysis with an id among c("pep_seq", "pep_seq_mod", "prot_acc", "gene"). A primary file contains normalized peptide or protein data and is among c("Peptide.txt", "Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt"). For analyses require the fields of significance p-values, the df will be one of c("Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt").
range_log2r	Numeric vector at length two. The argument specifies the range of the log2FC for use in the scaling normalization of standard deviation across samples. The default is between the 10th and the 90th quantiles.
range_int	Numeric vector at length two. The argument specifies the range of the intensity of reporter ions (including I000) for use in the scaling normalization of standard deviation across samples. The default is between the 5th and the 95th quantiles.
set_idx	Numeric. The index of a multiplex TMT experiment in metadata files such as label_scheme.xlsx and frac_scheme.xlsx.
injn_idx	Numeric. The index of LCMS_Inj in metadata files such as label_scheme.xlsx and frac_scheme.xlsx.

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