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Remove position analysis

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This commit is contained in:
Elias Projahn 2021-11-22 15:16:05 +01:00
parent 255123c74f
commit 599f09a52f
5 changed files with 15 additions and 52 deletions
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21
R/correlation.R
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@ -1,14 +1,12 @@
# Compute the mean correlation coefficient comparing gene distances with a set
# of reference genes.
correlation <- function(preset, use_positions = FALSE, progress = NULL) {
correlation <- function(preset, progress = NULL) {
species_ids <- preset$species_ids
gene_ids <- preset$gene_ids
reference_gene_ids <- preset$reference_gene_ids
cached(
"correlation",
c(species_ids, gene_ids, reference_gene_ids, use_positions),
{ # nolint
"correlation", c(species_ids, gene_ids, reference_gene_ids), {
# Prefilter distances by species.
distances <- geposan::distances[species %chin% species_ids]
@ -20,17 +18,10 @@ correlation <- function(preset, use_positions = FALSE, progress = NULL) {
# Make a column containing distance data for each species.
for (species_id in species_ids) {
species_data <- if (use_positions) {
setnames(distances[
species == species_id,
.(gene, position)
], "position", "distance")
} else {
distances[
species == species_id,
.(gene, distance)
]
}
species_data <- distances[
species == species_id,
.(gene, distance)
]
data <- merge(data, species_data, all.x = TRUE)
setnames(data, "distance", species_id)