% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/converters_PDtoMSstatsTMTFormat.R
\name{PDtoMSstatsTMTFormat}
\alias{PDtoMSstatsTMTFormat}
\title{Convert Proteome Discoverer output to MSstatsTMT format.}
\usage{
PDtoMSstatsTMTFormat(
  input,
  annotation,
  which.proteinid = "Protein.Accessions",
  useNumProteinsColumn = TRUE,
  useUniquePeptide = TRUE,
  rmPSM_withfewMea_withinRun = TRUE,
  rmProtein_with1Feature = FALSE,
  summaryforMultipleRows = sum,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  ...
)
}
\arguments{
\item{input}{PD report or a path to it.}

\item{annotation}{annotation with Run, Fraction, TechRepMixture, Mixture, Channel,
BioReplicate, Condition columns or a path to file. Refer to the example 'annotation' for the meaning of each column.}

\item{which.proteinid}{Use 'Protein.Accessions'(default) column for protein name. 'Master.Protein.Accessions' can be used instead to get the protein name with single protein.}

\item{useNumProteinsColumn}{logical, TRUE (default) removes shared peptides by information of # Proteins column in PSM sheet.}

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

\item{rmPSM_withfewMea_withinRun}{TRUE (default) will remove the features that have 1 or 2 measurements within each Run.}

\item{rmProtein_with1Feature}{TRUE will remove the proteins which have only 1 peptide and charge. Default is FALSE.}

\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.}

\item{...}{additional parameters to \code{data.table::fread}.}
}
\value{
\code{data.frame} of class \code{MSstatsTMT}
}
\description{
Convert Proteome Discoverer output to MSstatsTMT format.
}
\examples{
raw.pd = data.table::fread(system.file("tinytest/raw_data/PDTMT/pdtmt_input.csv",
                                      package = "MSstatsConvert"))
annotation.pd = data.table::fread(system.file("tinytest/raw_data/PDTMT/pd_annotation.csv",
                                      package = "MSstatsConvert"))
head(raw.pd)
head(annotation.pd)
input.pd <- PDtoMSstatsTMTFormat(raw.pd, annotation.pd)
head(input.pd)

}
