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

Reindent code to use just two spaces

Browse source
This commit is contained in:
Elias Projahn 2022-05-26 12:42:19 +02:00
parent a1e6147466
commit c04b6337e9
17 changed files with 1583 additions and 1582 deletions
Download patch file Download diff file Expand all files Collapse all files

58
R/method_proximity.R
View file

@ -11,38 +11,38 @@
#'
#' @export
proximity <- function(summarize = stats::median) {
method(
id = "proximity",
name = "Proximity",
description = "Proximity to telomeres",
function(preset, progress) {
species_ids <- preset$species_ids
gene_ids <- preset$gene_ids
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[,
.(combined_distance = as.double(summarize(distance))),
by = "gene"
]
# Compute the score as described above.
data <- data[,
.(combined_distance = as.double(summarize(distance))),
by = "gene"
]
# Normalize scores.
data[, score := 1 - combined_distance / max(combined_distance)]
# Normalize scores.
data[, score := 1 - combined_distance / max(combined_distance)]
progress(1.0)
progress(1.0)
result(
method = "proximity",
scores = data[, .(gene, score)],
details = list(data = data)
)
})
}
)
result(
method = "proximity",
scores = data[, .(gene, score)],
details = list(data = data)
)
})
}
)
}