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Restructure classes and their responsibilities

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Elias Projahn 2021-12-16 13:01:44 +01:00
parent 01ec301d6d
commit e2b93babe5
27 changed files with 974 additions and 634 deletions
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63
R/proximity.R
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@ -1,34 +1,39 @@
# 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(preset, progress = NULL) {
species_ids <- preset$species_ids
gene_ids <- preset$gene_ids
#' 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.
#'
#' @return An object of class `geposan_method`.
#'
#' @export
proximity <- function() {
method(
id = "proximity",
name = "Proximity",
description = "Proximity to telomeres",
function(preset, progress) {
species_ids <- preset$species_ids
gene_ids <- preset$gene_ids
cached("proximity", c(species_ids, gene_ids), {
# Prefilter distances by species and gene.
data <- geposan::distances[
species %chin% preset$species_ids & gene %chin% preset$gene_ids
]
cached("proximity", c(species_ids, gene_ids), {
# Prefilter distances by species and gene.
data <- geposan::distances[
species %chin% preset$species_ids &
gene %chin% preset$gene_ids
]
# Compute the score as described above.
data <- data[, .(mean_distance = mean(distance)), by = "gene"]
max_distance <- data[, max(mean_distance)]
data[, score := 1 - mean_distance / max_distance]
# Compute the score as described above.
data <- data[, .(mean_distance = mean(distance)), by = "gene"]
max_distance <- data[, max(mean_distance)]
data[, score := 1 - mean_distance / max_distance]
if (!is.null(progress)) {
# We do everything in one go, so it's not possible to report
# detailed progress information. As the method is relatively quick,
# this should not be a problem.
progress(1.0)
progress(1.0)
result(
method = "proximity",
scores = data[, .(gene, score)]
)
})
}
structure(
list(
results = data[, .(gene, score)]
),
class = "geposan_method_results"
)
})
)
}