add_prot_icover: Finds peptide abundance indexes.

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

Finds peptide abundance indexes.

Description

In relative to tryptic peptides.

Usage

add_prot_icover(df, id = "gene", pep_id = "pep_seq", max_len = 500L)

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.
pep_id	the column key of peptide sequences.
max_len	The maximum length of peptide sequence for consideration.

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