Rename data to input

data.R

@@ -1,68 +0,0 @@
-library(data.table)
-library(rlog)
-
-#' Merge genome data from files in `path` into `data.table`s.
-#'
-#' The result will be a list with named elements:
-#' - `genes` will be a table with metadata on human genes.
-#' - `species` will contain metadata on each species.
-#' - `distances` will contain each species' genes' distances to the telomere.
-#'
-#' @seealso [load_data_cached()]
-load_data <- function(path) {
-    genes <- fread(paste(path, "genes.tsv", sep = "/"))
-    original_species <- fread(paste(path, "species.csv", sep = "/"))
-
-    species <- data.table(
-        id = character(),
-        label = character(),
-        median_distance = numeric()
-    )
-
-    distances <- data.table(
-        species = character(),
-        gene = integer(),
-        distance = integer()
-    )
-
-    # Each file will contain data on one species.
-    file_names <- list.files(paste(path, "genomes", sep = "/"))
-    n_species <- length(file_names)
-
-    for (i in seq_along(file_names)) {
-        file_name <- file_names[i]
-        species_id <- strsplit(file_name, split = ".", fixed = TRUE)[[1]][1]
-        species_path <- paste(path, "genomes", file_name, sep = "/")
-
-        log_info(sprintf(
-            "Reading species %i/%i (%s)", i, n_species, species_id
-        ))
-
-        species_distances <- fread(species_path)
-
-        # Compute the median distance across all genes of this species and
-        # add it to the species table along other static data.
-        species <- rbindlist(list(species, data.table(
-            id = species_id,
-            label = original_species[id == species_id, label],
-            median_distance = median(species_distances[, dist])
-        )))
-
-        species_distances <- data.table(
-            species = species_id,
-            gene = species_distances[, geneid],
-            distance = species_distances[, dist]
-        )
-
-        distances <- rbindlist(list(distances, species_distances))
-    }
-
-    # Order species by their median distance.
-    setorder(species, median_distance)
-
-    list(
-        genes = genes,
-        species = species,
-        distances = distances
-    )
-}