johrpan/geposan
1
0
Fork 0
mirror of https://github.com/johrpan/geposan.git synced 2025-10-26 18:57:25 +01:00
Code Issues Projects Releases Packages Wiki Activity Actions

Implement all methods using positions additionally

Browse source
This commit is contained in:
Elias Projahn 2021-11-05 19:49:54 +01:00
parent 9cbc127177
commit cfc5e7a6bf
5 changed files with 222 additions and 167 deletions
Download patch file Download diff file Expand all files Collapse all files

12
R/clusteriness.R
View file

@ -36,11 +36,11 @@ clusteriness_priv <- function(data, height = 1000000) {
}
# Process genes clustering their distance to telomeres.
clusteriness <- function(preset, progress = NULL) {
clusteriness <- function(preset, use_positions = FALSE, progress = NULL) {
species_ids <- preset$species_ids
gene_ids <- preset$gene_ids
cached("clusteriness", c(species_ids, gene_ids), {
cached("clusteriness", c(species_ids, gene_ids, use_positions), {
results <- data.table(gene = gene_ids)
# Prefilter the input data by species.
@ -54,7 +54,13 @@ clusteriness <- function(preset, progress = NULL) {
# Perform the cluster analysis for one gene.
compute <- function(gene_id) {
score <- clusteriness_priv(distances[gene_id, distance])
data <- if (use_positions) {
distances[gene_id, position]
} else {
distances[gene_id, distance]
}
score <- clusteriness_priv(data)
if (!is.null(progress)) {
genes_done <<- genes_done + 1