purge_by_qt: Filters data groups by quantiles of CV

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

Filters data groups by quantiles of CV

Description

purge_by_qt replaces the data entries at CV > quantile with NA.

Usage

purge_by_qt(df, id, pt_cv = NULL, min_n = 1L, rm_allna = FALSE)

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").
id	Character string; one of pep_seq, pep_seq_mod, prot_acc and gene.
pt_cv	Numeric between 0 and 1; the percentile of CV. Values above the percentile threshold will be replaced with NA. The default is NULL with no data trimming by CV percentile. The precedence in data purging is pt_cv \ge max_cv \ge min_n.

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