% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/clean_MZMine.R
\name{.cleanRawMZMine}
\alias{.cleanRawMZMine}
\title{Clean raw MZMine files}
\usage{
.cleanRawMZMine(msstats_object, mzmine_annotations, sirius_annotations = NULL)
}
\arguments{
\item{msstats_object}{an object of class \code{MSstatsMZMineFiles}.}

\item{mzmine_annotations}{\code{data.frame} of MZMine spectral-library
annotations with columns \code{id}, \code{compound_name}, \code{score}. Required;
passing \code{NULL} raises an error. The highest-scoring \code{compound_name}
per feature (MSI Level 2 putative identification via MS/MS spectral
matching) is used as \code{ProteinName}.}

\item{sirius_annotations}{Optional \code{data.frame} of SIRIUS
\code{structure_identifications.tsv} output, or \code{NULL}. Only the
\code{mappingFeatureId} and \code{name} columns are read; score columns
(\code{ConfidenceScoreExact}, \code{ConfidenceScoreApproximate},
\code{SiriusScore}) are ignored in this release. When supplied, the
SIRIUS \code{name} (MSI Level 3, in-silico structure prediction) fills
\code{ProteinName} for features that received no MZMine compound name.
The schema is validated against SIRIUS 6 output; users on other
versions can rename columns to match. Pass \code{NULL} to disable.}
}
\value{
data.table
}
\description{
Operates on the column names produced by MZMine after MSstatsConvert's
internal column-name standardization (spaces collapsed and dots removed):
"row ID" becomes \code{rowID}, and each "\if{html}{\out{<sample>}} Peak area" becomes
\verb{<standardized-sample>Peakarea}.
}
\keyword{internal}
