% Generated by roxygen2: do not edit by hand
% Please edit documentation in
%   R/converters_ProteinProspectortoMSstatsTMTFormat.R
\name{ProteinProspectortoMSstatsTMTFormat}
\alias{ProteinProspectortoMSstatsTMTFormat}
\title{Generate MSstatsTMT required input format from Protein Prospector output}
\usage{
ProteinProspectortoMSstatsTMTFormat(
  input,
  annotation,
  useUniquePeptide = TRUE,
  removeFewMeasurements = TRUE,
  removeProtein_with1Feature = FALSE,
  summaryforMultipleRows = sum,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL
)
}
\arguments{
\item{input}{Input txt peptide report file from Protein Prospector with
"Keep Replicates", "Mods in Peptide", and "Protein Mods" options selected.}

\item{annotation}{data frame which contains column Run, Fraction,
TechRepMixture, Mixture, Channel, BioReplicate, Condition.}

\item{useUniquePeptide}{TRUE (default) removes peptides that are assigned for more than one proteins.
We assume to use unique peptide for each protein.}

\item{removeFewMeasurements}{TRUE (default) will remove the features that have 1 or 2 measurements across runs.}

\item{removeProtein_with1Feature}{TRUE will remove the proteins which have only 1 feature, which is the combination of peptide, precursor charge, fragment and charge. FALSE is default.}

\item{summaryforMultipleRows}{max or sum - when multiple PSMs identify
the same feature within a single MS run (duplicate PSMs), use the
highest (max) or sum of the duplicate intensities. Default is max for
label-free converters and sum for TMT converters. Note that this parameter
does NOT control collapsing across fractions of the same biological mixture.}

\item{use_log_file}{logical. If TRUE, information about data processing
will be saved to a file.}

\item{append}{logical. If TRUE, information about data processing will be added
to an existing log file.}

\item{verbose}{logical. If TRUE, information about data processing will be printed
to the console.}

\item{log_file_path}{character. Path to a file to which information about
data processing will be saved.
If not provided, such a file will be created automatically.
If \code{append = TRUE}, has to be a valid path to a file.}
}
\value{
data.frame of class "MSstatsTMT"
}
\description{
Generate MSstatsTMT required input format from Protein Prospector output
}
\examples{
input = system.file("tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt",
    package = "MSstatsConvert")
input = data.table::fread(input)
annot = system.file("tinytest/raw_data/ProteinProspector/Annotation.csv",
                                package = "MSstatsConvert")
annot = data.table::fread(annot)
output <- ProteinProspectortoMSstatsTMTFormat(input, annot)
head(output)

}
