readCurationFile.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/readCurationFile.R
\name{readCurationFile}
\alias{readCurationFile}
\title{Read curation file}
\usage{
readCurationFile(
  file.rds,
  file.curation = gsub(".rds$", ".csv", file.rds),
  remove.failed = FALSE,
  report.best.only = FALSE,
  min.ploidy = NULL,
  max.ploidy = NULL
)
}
\arguments{
\item{file.rds}{Output of the \code{\link{runAbsoluteCN}} function,
serialized with \code{saveRDS}.}

\item{file.curation}{Filename of a curation file that points to the correct
tumor purity and ploidy solution.}

\item{remove.failed}{Do not return solutions that failed.}

\item{report.best.only}{Only return correct/best solution (useful on low
memory machines when lots of samples are loaded).}

\item{min.ploidy}{Minimum ploidy to be considered. If \code{NULL}, all. Can
be used to automatically ignore unlikely solutions.}

\item{max.ploidy}{Maximum ploidy to be considered. If \code{NULL}, all. Can
be used to automatically ignore unlikely solutions.}
}
\value{
The return value of the corresponding \code{\link{runAbsoluteCN}}
call, but with the results array manipulated according the curation CSV file
and arguments of this function.
}
\description{
Function that can be used to read the curated output of the
\code{\link{runAbsoluteCN}} function.
}
\examples{

data(purecn.example.output)
file.rds <- "Sample1_PureCN.rds"
createCurationFile(file.rds)
# User can change the maximum likelihood solution manually in the generated
# CSV file. The correct solution is then loaded with readCurationFile.
purecn.curated.example.output <-readCurationFile(file.rds)

}
\seealso{
\code{\link{runAbsoluteCN} \link{createCurationFile}}
}
\author{
Markus Riester
}