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man/analyze.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/analyze.R
+\name{analyze}
+\alias{analyze}
+\title{Analyze by applying the specified preset.}
+\usage{
+analyze(preset)
+}
+\arguments{
+\item{preset}{The preset to use which can be created using \code{\link[=preset]{preset()}}.}
+}
+\value{
+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.
+}
+\description{
+Analyze by applying the specified preset.
+}

man/distances.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{distances}
+\alias{distances}
+\title{Information on gene positions across species.}
+\format{
+A \link{data.table} with 1390730 rows and 3 variables:
+\describe{
+\item{species}{Species ID}
+\item{gene}{Gene ID}
+\item{distance}{Distance to nearest telomere}
+}
+}
+\usage{
+distances
+}
+\description{
+This dataset contains each known value for a gene's distance to the telomeres
+per species. The data is sourced from Ensembl.
+}
+\keyword{datasets}

man/genes.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{genes}
+\alias{genes}
+\title{Information on human genes within the Ensembl database.}
+\format{
+A \link{data.table} with 60568 rows and 3 variables:
+\describe{
+\item{id}{Ensembl gene ID}
+\item{name}{The gene's HGNC name}
+\item{chrosome}{The human chromosome the gene is located on}
+\item{n_species}{Number of known species with the gene.}
+}
+}
+\usage{
+genes
+}
+\description{
+This includes only genes on the primary suggested assembly of the human
+nuclear DNA.
+}
+\keyword{datasets}

man/optimize_weights.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ranking.R
+\name{optimize_weights}
+\alias{optimize_weights}
+\title{Find the best weights to rank the results.}
+\usage{
+optimize_weights(results, methods, reference_gene_ids)
+}
+\arguments{
+\item{results}{Results from \code{\link[=analyze]{analyze()}} or \code{\link[=ranking]{ranking()}}.}
+
+\item{methods}{Methods to include in the score.}
+
+\item{reference_gene_ids}{IDs of the reference genes.}
+}
+\value{
+Named list pairing method names with their optimal weights.
+}
+\description{
+This function finds the optimal parameters to \code{\link[=ranking]{ranking()}} that result in the
+reference genes ranking particulary high.
+}

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.
+}
+}

man/ranking.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ranking.R
+\name{ranking}
+\alias{ranking}
+\title{Rank the results by computing a score.}
+\usage{
+ranking(results, weights)
+}
+\arguments{
+\item{results}{Results from \code{\link[=analyze]{analyze()}}.}
+
+\item{weights}{Named list pairing method names with weighting factors.}
+}
+\description{
+This function takes the result from \code{\link[=analyze]{analyze()}} and creates a score by
+computing a weighted mean across the different methods' results.
+}

man/species.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{species}
+\alias{species}
+\title{Information on included species from the Ensembl database.}
+\format{
+A \link{data.table} with 91 rows and 2 variables:
+\describe{
+\item{id}{Unique species ID}
+\item{name}{Human readable species name}
+}
+}
+\usage{
+species
+}
+\description{
+Information on included species from the Ensembl database.
+}
+\keyword{datasets}