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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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27
R/neural.R
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@ -25,10 +25,7 @@ neural <- function(preset, progress = NULL, seed = 49641) {
# Make a columns containing positions and distances for each
# species.
for (species_id in species_ids) {
species_data <- distances[
species == species_id,
.(gene, position, distance)
]
species_data <- distances[species == species_id, .(gene, distance)]
# Only include species with at least 25% known values. As
# positions and distances always coexist, we don't loose any
@ -46,26 +43,14 @@ neural <- function(preset, progress = NULL, seed = 49641) {
# However, this will of course lessen the significance of
# the results.
mean_position <- round(species_data[, mean(position)])
mean_distance <- round(species_data[, mean(distance)])
data[is.na(distance), `:=`(distance = mean_distance)]
data[is.na(distance), `:=`(
position = mean_position,
distance = mean_distance
)]
# Name the new column after the species.
setnames(data, "distance", species_id)
input_position <- sprintf("%s_position", species_id)
input_distance <- sprintf("%s_distance", species_id)
# Name the new columns after the species.
setnames(
data,
c("position", "distance"),
c(input_position, input_distance)
)
# Add the input variables to the buffer.
input_vars <- c(input_vars, input_position, input_distance)
# Add the input variable to the buffer.
input_vars <- c(input_vars, species_id)
}
}