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validate: Update and extend

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Elias Projahn 2022-01-26 11:38:39 +01:00
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man/validate.Rd
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@ -2,21 +2,38 @@
% Please edit documentation in R/validate.R
\name{validate}
\alias{validate}
\title{Perform cross-validation for the analysis.}
\title{Perform cross-validation for the ranking.}
\usage{
validate(analysis, progress = NULL)
validate(ranking, reference_gene_ids, method_ids, progress = NULL)
}
\arguments{
\item{analysis}{The analysis to validate.}
\item{ranking}{The ranking to validate.}
\item{reference_gene_ids}{The reference gene IDs whose ranking should be
validated.}
\item{method_ids}{IDs of the methods that were used.}
\item{progress}{An optional progress function that should accept a single
value between 0.0 and 1.0 for progress information.}
}
\value{
An object containing the mean absolute error and the mean percent
rank for the original analysis as well as the validation.
A validation object with the following items:
\describe{
\item{\code{validation}}{A \code{data.table} containing percentiles of the
comparison genes from the original ranking as well as their validation.
}
\item{\code{mean_score}}{The mean score of the genes.}
\item{\code{mean_percentile_original}}{The mean percentile of the genes in
the original ranking.
}
\item{\code{mean_percentile_validation}}{The mean percentile of the genes
when optimizing without themselves.
}
\item{\code{mean_error}}{The mean absolute error.}
}
}
\description{
This function reoptimizes the analysis leaving out one of the original
This function reoptimizes the ranking leaving out one of the original
reference genes at a time.
}