subset_fasta: Subsets fasta by accession type

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

Subsets fasta by accession type

Description

Not yet used.

Usage

subset_fasta(df, fasta, acc_type)

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).
acc_type	Character string; the type of protein accessions in one of c("refseq_acc", "uniprot_acc", "uniprot_id")

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