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analyze: Add optimization

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This commit is contained in:
Elias Projahn 2021-11-19 15:07:15 +01:00
parent b018838d37
commit 5a58f457a4
5 changed files with 63 additions and 32 deletions
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5
man/analyze.Rd
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@ -18,9 +18,8 @@ An object containing the results of the analysis with the following
items:
\describe{
\item{\code{preset}}{The preset that was used.}
\item{\code{results}}{A \link{data.table} with one row for each gene identified by
it's ID (\code{gene} column). The additional columns contain the resulting
scores per method and are named after the method IDs.}
\item{\code{weights}}{The optimal weights for ranking the reference genes.}
\item{\code{ranking}}{The optimal ranking created using the weights.}
}
}
\description{

13
man/preset.Rd
View file

@ -9,7 +9,8 @@ preset(
"correlation_positions", "neural", "neural_positions", "proximity"),
species_ids = NULL,
gene_ids = NULL,
reference_gene_ids = NULL
reference_gene_ids = NULL,
optimization_target = "mean_rank"
)
}
\arguments{
@ -20,6 +21,9 @@ preset(
\item{gene_ids}{IDs of genes to screen.}
\item{reference_gene_ids}{IDs of reference genes to compare to.}
\item{optimization_target}{Parameter of the reference genes that the ranking
should be optimized for.}
}
\value{
The preset to use with \code{\link[=analyze]{analyze()}}.
@ -47,4 +51,11 @@ telomere across species.
position data.
\item \code{proximity} Mean proximity to telomeres.
}
Available optimization targets are:
\itemize{
\item \code{mean} Mean rank of the reference genes.
\item \code{max} First rank of the reference genes.
\item \code{min} Last rank of the reference genes.
}
}