dblTrim: Data normalization

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

Data normalization

Description

dblTrim doubly trims the log2FC and reporter-ion intensity by the given ranges.

Usage

dblTrim(
  df,
  range_log2r = c(0, 100),
  range_int = c(0, 100),
  type_r = "N_log2_R",
  type_int = "N_I"
)

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.
type_r	Character string for recognizing the columns of log2FC.
type_int	Character string for recognizing the columns of intensity.

Value

A data frame.

qzhang503/proteoQ documentation built on March 16, 2024, 5:27 a.m.