johrpan/geposan
1
0
Fork 0
mirror of https://github.com/johrpan/geposan.git synced 2025-10-26 10:47:25 +01:00
Code Issues Projects Releases Packages Wiki Activity Actions

analyze: Add optimization

Browse source
This commit is contained in:
Elias Projahn 2021-11-19 15:07:15 +01:00
parent b018838d37
commit 5a58f457a4
5 changed files with 63 additions and 32 deletions
Download patch file Download diff file Expand all files Collapse all files

21
R/preset.R
View file

@ -21,10 +21,18 @@
#' position data.
#' - `proximity` Mean proximity to telomeres.
#'
#' Available optimization targets are:
#'
#' - `mean` Mean rank of the reference genes.
#' - `max` First rank of the reference genes.
#' - `min` Last rank of the reference genes.
#'
#' @param methods Methods to apply.
#' @param species_ids IDs of species to include.
#' @param gene_ids IDs of genes to screen.
#' @param reference_gene_ids IDs of reference genes to compare to.
#' @param optimization_target Parameter of the reference genes that the ranking
#' should be optimized for.
#'
#' @return The preset to use with [analyze()].
#'
@ -40,7 +48,8 @@ preset <- function(methods = c(
),
species_ids = NULL,
gene_ids = NULL,
reference_gene_ids = NULL) {
reference_gene_ids = NULL,
optimization_target = "mean_rank") {
# Count included species per gene.
genes_n_species <- geposan::distances[
species %chin% species_ids,
@ -61,7 +70,8 @@ preset <- function(methods = c(
methods = sort(methods),
species_ids = sort(species_ids),
gene_ids = sort(gene_ids_filtered),
reference_gene_ids = sort(reference_gene_ids)
reference_gene_ids = sort(reference_gene_ids),
optimization_target = optimization_target
),
class = "geposan_preset"
)
@ -87,9 +97,14 @@ print.geposan_preset <- function(x, ...) {
))
cat(sprintf(
"\n Comparison data: %i reference genes\n",
"\n Comparison data: %i reference genes",
length(x$reference_gene_ids)
))
cat(sprintf(
"\n Optimization target: %s\n",
x$optimization_target
))
invisible(x)
}