filterData: Filters rows by variance quantiles

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

Filters rows by variance quantiles

Description

Filters rows by variance quantiles

Usage

filterData(df, cols = NULL, var_cutoff = 0.001)

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").
cols	Column indexes
var_cutoff	Numeric; the cut-off in the variances of log2FC. Entries with variances smaller than the threshold will be excluded from linear modeling. The default is 1E-3.

qzhang503/proteoQ documentation built on April 13, 2025, 8:31 a.m.