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Add species adjacency method

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This commit is contained in:
Elias Projahn 2022-01-17 20:11:07 +01:00
parent c8f1e522f9
commit 53f955f3da
6 changed files with 202 additions and 14 deletions
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23
R/adjacency.R
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@ -24,16 +24,23 @@ densest <- function(data) {
#' Score genes based on their proximity to the reference genes.
#'
#' @param estimate A function that will be used to summarize the distance
#' values for each gene. See [densest()] for the default implementation.
#' @param combination A function that will be used to combine the different
#' In this case, the distance data that is available for one gene is first
#' combined. The resulting value is compared to the reference genes and
#' determines the gene's score in relation to other genes.
#'
#' @param distance_estimate A function that will be used to summarize the
#' distance values for each gene. See [densest()] for the default
#' implementation.
#' @param summarize A function that will be used to combine the different
#' distances to the reference genes. By default [min()] is used. That means
#' the distance to the nearest reference gene will be scored.
#'
#' @return An object of class `geposan_method`.
#'
#' @seealso [species_adjacency()]
#'
#' @export
adjacency <- function(estimate = densest, combination = min) {
adjacency <- function(distance_estimate = densest, summarize = min) {
method(
id = "adjacency",
name = "Adjacency",
@ -49,15 +56,15 @@ adjacency <- function(estimate = densest, combination = min) {
species_ids,
gene_ids,
reference_gene_ids,
estimate,
combination
distance_estimate,
summarize
),
{ # nolint
# Filter distances by species and gene and summarize each
# gene's distance values using the estimation function.
data <- geposan::distances[
species %chin% species_ids & gene %chin% gene_ids,
.(distance = as.numeric(estimate(distance))),
.(distance = as.numeric(distance_estimate(distance))),
by = gene
]
@ -70,7 +77,7 @@ adjacency <- function(estimate = densest, combination = min) {
.(difference = abs(distance_value - distance))
]
combination(differences$difference)
summarize(differences$difference)
}
# Compute the differences to the reference genes.