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man/preset.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/analyze.R
+\name{preset}
+\alias{preset}
+\title{Create a new preset.}
+\usage{
+preset(methods, species, genes, reference_genes)
+}
+\arguments{
+\item{methods}{IDs of methods to apply.}
+
+\item{species}{IDs of species to include.}
+
+\item{genes}{IDs of genes to screen.}
+
+\item{reference_genes}{IDs of reference genes to compare to.}
+}
+\value{
+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.
+}
+\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{proximity} Mean proximity to telomeres.
+\item \code{neural} Assessment by neural network.
+}
+}