annotPrn: Adds protein annotation

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

Adds protein annotation

Description

annotPrn cross-referencing proteins among uniprot_acc, uniprot_id, refseq and entrez.

Usage

annotPrn(df, fasta, entrez)

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").
fasta	Character string(s) to the name(s) of fasta file(s) with prepended directory path. The fasta database(s) need to match those used in MS/MS ion search. There is no default and users need to provide the correct file path(s) and name(s).
entrez	Character string(s) to the name(s) of entrez file(s) with prepended directory path. At the NULL default, a convenience lookup is available for species among c("human", "mouse", "rat"). For other species, users need to provide the file path(s) and name(s) for the lookup table(s). See also Uni2Entrez and Ref2Entrez for preparing custom entrez files.

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