annotPrn.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/utils.R
\name{annotPrn}
\alias{annotPrn}
\title{Adds protein annotation}
\usage{
annotPrn(df, fasta, entrez)
}
\arguments{
\item{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
\code{id} among \code{c("pep_seq", "pep_seq_mod", "prot_acc", "gene")}. A
primary file contains normalized peptide or protein data and is among
\code{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 \code{df} will be one of
\code{c("Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein_pVal.txt",
"protein_impNA_pVal.txt")}.}

\item{fasta}{Character string(s) to the name(s) of fasta file(s) with
prepended directory path. The \code{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).}

\item{entrez}{Character string(s) to the name(s) of entrez file(s) with
prepended directory path. At the \code{NULL} default, a convenience lookup
is available for species among \code{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 \code{\link{Uni2Entrez}} and \code{\link{Ref2Entrez}} for
preparing custom entrez files.}
}
\description{
\code{annotPrn} cross-referencing proteins among \code{uniprot_acc},
\code{uniprot_id}, \code{refseq} and \code{entrez}.
}