commit c52d42c2b6cea2bc038b0fee2e75e3218a57e04f
Author: Elias Projahn <elias@johrpan.de>
Date:   Tue Oct 19 13:39:55 2021 +0200

    Initial commit

diff --git a/.Rbuildignore b/.Rbuildignore
new file mode 100644
index 0000000..38ff65d
--- /dev/null
+++ b/.Rbuildignore
@@ -0,0 +1,4 @@
+^geposan\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$
+^scripts$
diff --git a/.gitignore b/.gitignore
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--- /dev/null
+++ b/.gitignore
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+.Rproj.user
diff --git a/DESCRIPTION b/DESCRIPTION
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--- /dev/null
+++ b/DESCRIPTION
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+Package: geposan
+Title: Gene Position Analysis
+Version: 0.0.0.9000
+Authors@R:
+    person(
+        "Elias",
+        "Projahn",
+        email = "elias@johrpan.de",
+        role = c("aut", "cre"),
+    )
+Description: Analyze genes based on their position across species. This package
+    includes gene data from Ensembl. It provides multiple methods to use that
+    data to find genes that score well in comparison with a set of reference
+    genes.
+License: GPL (>= 3)
+Encoding: UTF-8
+LazyData: true
+LazyDataCompression: xz
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.2
+Depends:
+    R (>= 2.10)
+Imports:
+    data.table,
+    neuralnet
+Suggests:
+    biomaRt,
+    rlog,
+    stringr,
+    usethis
diff --git a/LICENSE.md b/LICENSE.md
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index 0000000..175443c
--- /dev/null
+++ b/LICENSE.md
@@ -0,0 +1,595 @@
+GNU General Public License
+==========================
+
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+THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
+EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER
+EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE
+QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE
+DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+### 16. Limitation of Liability
+
+IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY
+COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS
+PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL,
+INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
+PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE
+OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE
+WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+### 17. Interpretation of Sections 15 and 16
+
+If the disclaimer of warranty and limitation of liability provided above cannot be
+given local legal effect according to their terms, reviewing courts shall apply local
+law that most closely approximates an absolute waiver of all civil liability in
+connection with the Program, unless a warranty or assumption of liability accompanies
+a copy of the Program in return for a fee.
+
+_END OF TERMS AND CONDITIONS_
+
+## How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible use to
+the public, the best way to achieve this is to make it free software which everyone
+can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach them
+to the start of each source file to most effectively state the exclusion of warranty;
+and each file should have at least the “copyright” line and a pointer to
+where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program does terminal interaction, make it output a short notice like this
+when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type 'show c' for details.
+
+The hypothetical commands `show w` and `show c` should show the appropriate parts of
+the General Public License. Of course, your program's commands might be different;
+for a GUI interface, you would use an “about box”.
+
+You should also get your employer (if you work as a programmer) or school, if any, to
+sign a “copyright disclaimer” for the program, if necessary. For more
+information on this, and how to apply and follow the GNU GPL, see
+&lt;<http://www.gnu.org/licenses/>&gt;.
+
+The GNU General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may consider it
+more useful to permit linking proprietary applications with the library. If this is
+what you want to do, use the GNU Lesser General Public License instead of this
+License. But first, please read
+&lt;<http://www.gnu.org/philosophy/why-not-lgpl.html>&gt;.
diff --git a/NAMESPACE b/NAMESPACE
new file mode 100644
index 0000000..1d3b3d4
--- /dev/null
+++ b/NAMESPACE
@@ -0,0 +1,7 @@
+# Generated by roxygen2: do not edit by hand
+
+export(analyze)
+export(optimize_weights)
+export(preset)
+export(ranking)
+import(data.table)
diff --git a/R/analyze.R b/R/analyze.R
new file mode 100644
index 0000000..1389b52
--- /dev/null
+++ b/R/analyze.R
@@ -0,0 +1,72 @@
+#' Create a new preset.
+#'
+#' 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.
+#'
+#' Available methods are:
+#'
+#'  - `clusteriness` How much the gene distances cluster across species.
+#'  - `correlation` The mean correlation with the reference genes.
+#'  - `proximity` Mean proximity to telomeres.
+#'  - `neural` Assessment by neural network.
+#'
+#' @param methods IDs of methods to apply.
+#' @param species IDs of species to include.
+#' @param genes IDs of genes to screen.
+#' @param reference_genes IDs of reference genes to compare to.
+#'
+#' @return The preset to use with [analyze()].
+#'
+#' @export
+preset <- function(methods, species, genes, reference_genes) {
+    list(
+        method_ids = methods,
+        species_ids = species,
+        gene_ids = genes,
+        reference_gene_ids = reference_genes
+    )
+}
+
+#' Analyze by applying the specified preset.
+#'
+#' @param preset The preset to use which can be created using [preset()].
+#'
+#' @return A [data.table] with one row for each gene identified by it's ID
+#'   (`gene` column). The additional columns contain the resulting scores per
+#'   method and are named after the method IDs.
+#'
+#' @export
+analyze <- function(preset) {
+    # Available methods by ID.
+    #
+    # A method describes a way to perform a computation on gene distance data
+    # that results in a single score per gene. The function should accept the
+    # preset to apply as a single parameter (see [preset()]).
+    #
+    # The function should return a [data.table] with the following columns:
+    #
+    #  - `gene` Gene ID of the processed gene.
+    #  - `score` Score for the gene between 0.0 and 1.0.
+    methods <- list(
+        "clusteriness" = clusteriness,
+        "correlation" = correlation,
+        "proximity" = proximity,
+        "neural" = neural
+    )
+
+    results <- data.table(gene = genes$id)
+
+    for (method_id in preset$method_ids) {
+        method_results <- methods[[method_id]](distances, preset)
+        setnames(method_results, "score", method_id)
+
+        results <- merge(
+            results,
+            method_results,
+            by = "gene"
+        )
+    }
+
+    results
+}
diff --git a/R/clusteriness.R b/R/clusteriness.R
new file mode 100644
index 0000000..9f8e74e
--- /dev/null
+++ b/R/clusteriness.R
@@ -0,0 +1,54 @@
+# Perform a cluster analysis.
+#
+# This function will cluster the data using `hclust` and `cutree` (with the
+# specified height). Every cluster with at least two members qualifies for
+# further analysis. Clusters are then ranked based on their size in relation
+# to the number of values. The return value is a final score between zero and
+# one. Lower ranking clusters contribute less to this score.
+clusteriness_priv <- function(data, height = 1000000) {
+    n <- length(data)
+
+    # Return a score of 0.0 if there is just one or no value at all.
+    if (n < 2) {
+        return(0.0)
+    }
+
+    # Cluster the data and compute the cluster sizes.
+
+    tree <- stats::hclust(stats::dist(data))
+    clusters <- stats::cutree(tree, h = height)
+    cluster_sizes <- sort(tabulate(clusters), decreasing = TRUE)
+
+    # Compute the "clusteriness" score.
+
+    score <- 0.0
+
+    for (i in seq_along(cluster_sizes)) {
+        cluster_size <- cluster_sizes[i]
+
+        if (cluster_size >= 2) {
+            cluster_score <- cluster_size / n
+            score <- score + cluster_score / i
+        }
+    }
+
+    score
+}
+
+# Process genes clustering their distance to telomeres.
+clusteriness <- function(distances, preset) {
+    results <- data.table(gene = preset$gene_ids)
+
+    # Prefilter the input data by species.
+    distances <- distances[species %chin% preset$species_ids]
+
+    # Add an index for quickly accessing data per gene.
+    setkey(distances, gene)
+
+    # Perform the cluster analysis for one gene.
+    compute <- function(gene_id) {
+        clusteriness_priv(distances[gene_id, distance])
+    }
+
+    results[, score := compute(gene), by = 1:nrow(results)]
+}
diff --git a/R/correlation.R b/R/correlation.R
new file mode 100644
index 0000000..040b4b5
--- /dev/null
+++ b/R/correlation.R
@@ -0,0 +1,61 @@
+# Compute the mean correlation coefficient comparing gene distances with a set
+# of reference genes.
+correlation <- function(distances, preset) {
+    results <- data.table(gene = preset$gene_ids)
+    reference_gene_ids <- preset$reference_gene_ids
+    reference_count <- length(reference_gene_ids)
+
+    # Prefilter distances by species.
+    distances <- distances[species %chin% preset$species_ids]
+
+    # Add an index for quickly accessing data per gene.
+    setkey(distances, gene)
+
+    # Prepare the reference genes' data.
+    reference_distances <- distances[gene %chin% reference_gene_ids]
+
+    # Perform the correlation for one gene.
+    compute <- function(gene_id) {
+        gene_distances <- distances[gene_id]
+        gene_species_count <- nrow(gene_distances)
+
+        # Return a score of 0.0 if there is just one or no value at all.
+        if (gene_species_count <= 1) {
+            return(0.0)
+        }
+
+        # Buffer for the sum of correlation coefficients.
+        correlation_sum <- 0
+
+        # Correlate with all reference genes but not with the gene itself.
+        for (reference_gene_id in
+             reference_gene_ids[reference_gene_ids != gene_id]) {
+            data <- merge(
+                gene_distances,
+                reference_distances[reference_gene_id],
+                by = "species"
+            )
+
+            # Skip this reference gene, if there are not enough value pairs.
+            # This will lessen the final score, because it effectively
+            # represents a correlation coefficient of 0.0.
+            if (nrow(data) <= 1) {
+                next
+            }
+
+            # Order data by the reference gene's distance to get a monotonic
+            # relation.
+            setorder(data, distance.y)
+
+            correlation_sum <- correlation_sum + abs(stats::cor(
+                data[, distance.x], data[, distance.y],
+                method = "spearman"
+            ))
+        }
+
+        # Compute the score as the mean correlation coefficient.
+        score <- correlation_sum / reference_count
+    }
+
+    results[, score := compute(gene), by = 1:nrow(results)]
+}
diff --git a/R/data.R b/R/data.R
new file mode 100644
index 0000000..eaa1686
--- /dev/null
+++ b/R/data.R
@@ -0,0 +1,35 @@
+#' Information on included species from the Ensembl database.
+#'
+#' @format A [data.table] with 91 rows and 2 variables:
+#' \describe{
+#'   \item{id}{Unique species ID}
+#'   \item{name}{Human readable species name}
+#' }
+"species"
+
+#' Information on human genes within the Ensembl database.
+#'
+#' This includes only genes on the primary suggested assembly of the human
+#' nuclear DNA.
+#'
+#' @format A [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.}
+#' }
+"genes"
+
+#' Information on gene positions across species.
+#'
+#' This dataset contains each known value for a gene's distance to the telomeres
+#' per species. The data is sourced from Ensembl.
+#'
+#' @format A [data.table] with 1390730 rows and 3 variables:
+#' \describe{
+#'   \item{species}{Species ID}
+#'   \item{gene}{Gene ID}
+#'   \item{distance}{Distance to nearest telomere}
+#' }
+"distances"
diff --git a/R/neural.R b/R/neural.R
new file mode 100644
index 0000000..5618009
--- /dev/null
+++ b/R/neural.R
@@ -0,0 +1,96 @@
+# Find genes by training a neural network on reference position data.
+#
+# @param seed A seed to get reproducible results.
+neural <- function(distances, preset, seed = 448077) {
+    species_ids <- preset$species_ids
+    reference_gene_ids <- preset$reference_gene_ids
+
+    set.seed(seed)
+    gene_count <- length(preset$gene_ids)
+
+    # Prefilter distances by species.
+    distances <- distances[species %chin% species_ids]
+
+    # Input data for the network. This contains the gene ID as an identifier
+    # as well as the per-species gene distances as input variables.
+    data <- data.table(gene = preset$gene_ids)
+
+    # Buffer to keep track of species included in the computation. Species
+    # from `species_ids` may be excluded if they don't have enough data.
+    species_ids_included <- NULL
+
+    # Make a column containing distance data for each species.
+    for (species_id in species_ids) {
+        species_distances <- distances[species == species_id, .(gene, distance)]
+
+        # Only include species with at least 25% known values.
+
+        species_distances <- stats::na.omit(species_distances)
+
+        if (nrow(species_distances) >= 0.25 * gene_count) {
+            species_ids_included <- c(species_ids_included, species_id)
+            data <- merge(data, species_distances, all.x = TRUE)
+
+            # Replace missing data with mean values. The neural network can't
+            # handle NAs in a meaningful way. Choosing extreme values here
+            # would result in heavily biased results. Therefore, the mean value
+            # is chosen as a compromise. However, this will of course lessen the
+            # significance of the results.
+
+            mean_distance <- round(species_distances[, mean(distance)])
+            data[is.na(distance), distance := mean_distance]
+
+            # Name the new column after the species.
+            setnames(data, "distance", species_id)
+        }
+    }
+
+    # Extract the reference genes.
+
+    reference_data <- data[gene %chin% reference_gene_ids]
+    reference_data[, neural := 1.0]
+
+    # Take out random samples from the remaining genes. This is another
+    # compromise with a negative impact on significance. Because there is no
+    # information on genes with are explicitely *not* TPE-OLD genes, we have to
+    # assume that a random sample of genes has a low probability of including
+    # TPE-OLD genes.
+
+    without_reference_data <- data[!gene %chin% reference_gene_ids]
+
+    reference_samples <- without_reference_data[
+        sample(
+            nrow(without_reference_data),
+            nrow(reference_data)
+        )
+    ]
+
+    reference_samples[, neural := 0.0]
+
+    # Merge training data. The training data includes all reference genes as
+    # well as an equal number of random sample genes.
+    training_data <- rbindlist(list(reference_data, reference_samples))
+
+    # Construct and train the neural network.
+
+    nn_formula <- stats::as.formula(sprintf(
+        "neural~%s",
+        paste(species_ids_included, collapse = "+")
+    ))
+
+    layer1 <- length(species_ids) * 0.66
+    layer2 <- layer1 * 0.66
+    layer3 <- layer2 * 0.66
+
+    nn <- neuralnet::neuralnet(
+        nn_formula,
+        training_data,
+        hidden = c(layer1, layer2, layer3),
+        linear.output = FALSE
+    )
+
+    # Return the resulting scores given by applying the neural network.
+
+    data[, score := neuralnet::compute(nn, data)$net.result]
+    data[, .(gene, score)]
+}
diff --git a/R/proximity.R b/R/proximity.R
new file mode 100644
index 0000000..a64e398
--- /dev/null
+++ b/R/proximity.R
@@ -0,0 +1,18 @@
+# Score the mean distance of genes to the telomeres across species.
+#
+# A score will be given to each gene such that 0.0 corresponds to the maximal
+# mean distance across all genes and 1.0 corresponds to a distance of 0.
+proximity <- function(distances, preset) {
+    # Prefilter distances by species and gene.
+    distances <- distances[
+        species %chin% preset$species_ids & gene %chin% preset$gene_ids
+    ]
+
+    # Compute the score as described above.
+
+    distances <- distances[, .(mean_distance = mean(distance)), by = "gene"]
+    max_distance <- distances[, max(mean_distance)]
+    distances[, score := 1 - mean_distance / max_distance]
+
+    distances[, .(gene, score)]
+}
diff --git a/R/ranking.R b/R/ranking.R
new file mode 100644
index 0000000..a4ab21b
--- /dev/null
+++ b/R/ranking.R
@@ -0,0 +1,63 @@
+#' Rank the results by computing a score.
+#'
+#' This function takes the result from [analyze()] and creates a score by
+#' computing a weighted mean across the different methods' results.
+#'
+#' @param results Results from [analyze()].
+#' @param weights Named list pairing method names with weighting factors.
+#'
+#' @result The input data with an additional column containing the score and
+#'   another column containing the rank.
+#'
+#' @export
+ranking <- function(results, weights) {
+    results <- copy(results)
+    results[, score := 0.0]
+
+    for (method in names(weights)) {
+        weighted <- weights[[method]] * results[, ..method]
+        results[, score := score + weighted]
+    }
+
+    # Normalize scores to be between 0.0 and 1.0.
+    results[, score := score / sum(unlist(weights))]
+
+    setorder(results, -score)
+    results[, rank := .I]
+}
+
+#' Find the best weights to rank the results.
+#'
+#' This function finds the optimal parameters to [ranking()] that result in the
+#' reference genes ranking particulary high.
+#'
+#' @param results Results from [analyze()] or [ranking()].
+#' @param methods Methods to include in the score.
+#' @param reference_gene_ids IDs of the reference genes.
+#'
+#' @returns Named list pairing method names with their optimal weights.
+#'
+#' @export
+optimize_weights <- function(results, methods, reference_gene_ids) {
+    # Create the named list from the factors vector.
+    weights <- function(factors) {
+        result <- NULL
+
+        mapply(function(method, factor) {
+            result[[method]] <<- factor
+        }, methods, factors)
+
+        result
+    }
+
+    # Compute the mean rank of the reference genes when applying the weights.
+    mean_rank <- function(factors) {
+        data <- ranking(results, weights(factors))
+        data[gene %chin% reference_gene_ids, mean(rank)]
+    }
+
+    factors <- stats::optim(rep(1.0, length(methods)), mean_rank)$par
+    total_weight <- sum(factors)
+
+    weights(factors / total_weight)
+}
diff --git a/R/utils.R b/R/utils.R
new file mode 100644
index 0000000..887a466
--- /dev/null
+++ b/R/utils.R
@@ -0,0 +1,3 @@
+# This is needed to make data.table's symbols available within the package.
+#' @import data.table
+NULL
diff --git a/data/distances.rda b/data/distances.rda
new file mode 100644
index 0000000..8cf319f
Binary files /dev/null and b/data/distances.rda differ
diff --git a/data/genes.rda b/data/genes.rda
new file mode 100644
index 0000000..793f8c1
Binary files /dev/null and b/data/genes.rda differ
diff --git a/data/species.rda b/data/species.rda
new file mode 100644
index 0000000..87b6259
Binary files /dev/null and b/data/species.rda differ
diff --git a/man/analyze.Rd b/man/analyze.Rd
new file mode 100644
index 0000000..99d9211
--- /dev/null
+++ b/man/analyze.Rd
@@ -0,0 +1,19 @@
+% 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.
+}
diff --git a/man/distances.Rd b/man/distances.Rd
new file mode 100644
index 0000000..5ca856f
--- /dev/null
+++ b/man/distances.Rd
@@ -0,0 +1,22 @@
+% 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}
diff --git a/man/genes.Rd b/man/genes.Rd
new file mode 100644
index 0000000..5cf2454
--- /dev/null
+++ b/man/genes.Rd
@@ -0,0 +1,23 @@
+% 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}
diff --git a/man/optimize_weights.Rd b/man/optimize_weights.Rd
new file mode 100644
index 0000000..ed21a06
--- /dev/null
+++ b/man/optimize_weights.Rd
@@ -0,0 +1,22 @@
+% 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.
+}
diff --git a/man/preset.Rd b/man/preset.Rd
new file mode 100644
index 0000000..ea8c743
--- /dev/null
+++ b/man/preset.Rd
@@ -0,0 +1,34 @@
+% 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.
+}
+}
diff --git a/man/ranking.Rd b/man/ranking.Rd
new file mode 100644
index 0000000..40b657a
--- /dev/null
+++ b/man/ranking.Rd
@@ -0,0 +1,17 @@
+% 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.
+}
diff --git a/man/species.Rd b/man/species.Rd
new file mode 100644
index 0000000..66e5386
--- /dev/null
+++ b/man/species.Rd
@@ -0,0 +1,20 @@
+% 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}
diff --git a/scripts/ensembl.R b/scripts/ensembl.R
new file mode 100644
index 0000000..3807cbc
--- /dev/null
+++ b/scripts/ensembl.R
@@ -0,0 +1,154 @@
+library(data.table)
+
+rlog::log_info("Connecting to Ensembl API")
+
+#' Object to access the Ensembl API.
+ensembl <- biomaRt::useEnsembl("ensembl")
+
+# Retrieve species information.
+
+rlog::log_info("Retrieving species information")
+ensembl_datasets <- data.table(biomaRt::listDatasets(ensembl))
+
+# Filter out species ID and name from the result.
+species <- ensembl_datasets[, .(
+    id = stringr::str_match(dataset, "(.*)_gene_ensembl")[, 2],
+    name = stringr::str_match(description, "(.*) genes \\(.*\\)")[, 2]
+)]
+
+#' Get all chromosome names for an Ensembl dataset.
+#'
+#' Valid chromosome names include decimal numbers as well as typical sex
+#' chromosome names (X, Y, W and Z).
+get_chromosome_names <- function(dataset) {
+    chromosome_names <- biomaRt::listFilterOptions(dataset, "chromosome_name")
+    chromosome_names[stringr::str_which(chromosome_names, "^[0-9]+|[XYWZ]$")]
+}
+
+# Retrieve information on human genes. This will only include genes on
+# assembled chromosomes. Chromosomes are filtered using get_chromosome_names().
+
+rlog::log_info("Retrieving information on human genes")
+dataset <- biomaRt::useDataset("hsapiens_gene_ensembl", mart = ensembl)
+
+human_data <- data.table(biomaRt::getBM(
+    attributes = c(
+        "ensembl_gene_id",
+        "hgnc_symbol",
+        "chromosome_name",
+        "start_position",
+        "end_position"
+    ),
+    filters = "chromosome_name",
+    values = get_chromosome_names(dataset),
+    mart = dataset
+))
+
+# Remove duplicated gene IDs (at the time of writing, there are a handful).
+human_data <- unique(human_data, by = "ensembl_gene_id")
+
+# Only keep relevant information on genes.
+genes <- human_data[, .(
+    id = ensembl_gene_id,
+    name = hgnc_symbol,
+    chromosome = chromosome_name
+)]
+
+# Retrieve gene distance data across species.
+
+rlog::log_info("Retrieving distance data")
+
+# Handle the human first, as we already retrieved the data and don't need to
+# filter based on orthologies.
+
+human_data[, chromosome_length := max(end_position), by = chromosome_name]
+
+distances <- human_data[, .(
+    species = "hsapiens",
+    gene = ensembl_gene_id,
+    distance = pmin(
+        start_position,
+        chromosome_length - end_position
+    )
+)]
+
+# Iterate through all other species and retrieve their distance data.
+for (species_id in species[!id == "hsapiens", id]) {
+    rlog::log_info(sprintf("Loading species \"%s\"", species_id))
+
+    dataset <- biomaRt::useDataset(
+        sprintf("%s_gene_ensembl", species_id),
+        mart = ensembl
+    )
+
+    # Besides the attributes that are always present, we need to check for
+    # human orthologs. Some species don't have that information and will be
+    # skipped.
+    if (!"hsapiens_homolog_ensembl_gene" %chin%
+        biomaRt::listAttributes(dataset, what = "name")) {
+
+        rlog::log_info("No data on human orthologs")
+        species <- species[id != species_id]
+
+        next
+    }
+
+    chromosome_names <- get_chromosome_names(dataset)
+
+    # Skip the species, if there are no assembled chromosomes.
+    if (length(chromosome_names) <= 0) {
+        rlog::log_info("No matching chromosome assemblies")
+        species <- species[id != species_id]
+
+        next
+    }
+
+    # Retrieve information on all genes of the current species, that have
+    # human orthologs. This is called "homolog" in the Ensembl schema.
+    species_distances <- data.table(biomaRt::getBM(
+        attributes = c(
+            "hsapiens_homolog_ensembl_gene",
+            "chromosome_name",
+            "start_position",
+            "end_position"
+        ),
+        filters = c("with_hsapiens_homolog", "chromosome_name"),
+        values = list(TRUE, chromosome_names),
+        mart = dataset
+    ))
+
+    # Only include one ortholog per human gene.
+    species_distances <- unique(
+        species_distances,
+        by = "hsapiens_homolog_ensembl_gene"
+    )
+
+    # Precompute the genes' distance to the nearest telomere.
+
+    species_distances[,
+        chromosome_length := max(end_position),
+        by = chromosome_name
+    ]
+
+    species_distances <- species_distances[, .(
+        species = species_id,
+        gene = hsapiens_homolog_ensembl_gene,
+        distance = pmin(
+            start_position,
+            chromosome_length - end_position
+        )
+    )]
+
+    distances <- rbindlist(list(distances, species_distances))
+}
+
+# Add information on number of species per gene.
+
+genes_n_species <- distances[, .(n_species = .N), by = "gene"]
+genes <- merge(genes, genes_n_species, by.x = "id", by.y = "gene")
+
+# Save data in the appropriate place.
+
+usethis::use_data(species, overwrite = TRUE)
+usethis::use_data(genes, overwrite = TRUE)
+usethis::use_data(distances, overwrite = TRUE)