purge_by_cv: Filters data groups by a CV cut-off

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

Filters data groups by a CV cut-off

Description

purge_by_cv replaces the data entries at group CV > max_cv to NA.

Usage

purge_by_cv(df, id, max_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.
max_cv	Numeric; the cut-off in maximum CV. Values above the threshold will be replaced with NA. The default is NULL with no data trimming by max CV.
min_n	Positive integer. When calling from purgePSM, peptide entries in PSM tables with the number of identifying PSMs smaller than min_n will be replaced with NA. When calling from purgePep, protein entries in peptide tables with the number of identifying peptides smaller than min_n will be replaced with NA.
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.

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