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preset: Remove min_n_species customization

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Elias Projahn 2021-11-18 12:30:19 +01:00
parent 33056bfa40
commit de1c1ed40e
3 changed files with 48 additions and 31 deletions
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25
man/preset.Rd
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@ -5,10 +5,10 @@
\title{Create a new preset.}
\usage{
preset(
methods = c("clusteriness", "correlation", "neural", "proximity"),
methods = c("clusteriness", "clusteriness_positions", "correlation",
"correlation_positions", "neural", "neural_positions", "proximity"),
species_ids = NULL,
gene_ids = NULL,
min_n_species = 10,
reference_gene_ids = NULL
)
}
@ -19,9 +19,6 @@ preset(
\item{gene_ids}{IDs of genes to screen.}
\item{min_n_species}{Minimum number of orthologs that a gene should have to
be included in the analysis.}
\item{reference_gene_ids}{IDs of reference genes to compare to.}
}
\value{
@ -30,14 +27,24 @@ The preset to use with \code{\link[=analyze]{analyze()}}.
\description{
A preset is used to specify which methods and inputs should be used for an
analysis. Note that the genes to process should normally include the
reference genes to be able to assess the results later.
reference genes to be able to assess the results later. The genes will be
filtered based on how many species have data for them. Genes which only have
orthologs for less than 25\% of the input species will be excluded from the
preset and the analyis.
}
\details{
Available methods are:
\itemize{
\item \code{clusteriness} How much the gene distances cluster across species.
\item \code{correlation} The mean correlation with the reference genes.
\item \code{clusteriness} How much the gene distances to the nearest telomere
cluster across species.
\item \code{clusteriness_positions} The same as \code{clusteriness} but using absolute
gene positions instead of distances.
\item \code{correlation} The mean correlation of gene distances to the nearest
telomere across species.
\item \code{correlation_positions} Correlation using position data.
\item \code{neural} Assessment by neural network trained using distances.
\item \code{neural_positions} Assessment by neural network trained using absolute
position data.
\item \code{proximity} Mean proximity to telomeres.
\item \code{neural} Assessment by neural network.
}
}