Initial commit

data.R

@@ -0,0 +1,76 @@
+library(data.table)
+
+source("species.R")
+
+#' Load and preprocess input data from `path`.
+#'
+#' A file named `cache.rds` will be created within that directory to reuse the
+#' results for future runs. To forcefully recompute, delete that file.
+#'
+#' @seealso [load_data()]
+load_data_cached <- function(path) {
+    cache_file <- paste(path, "cache.rds", sep = "/")
+
+    if (!file.exists(cache_file)) {
+        # If the cache file doesn't exist, we have to do the computation.
+        data <- load_data("input")
+
+        # The results are cached for the next run.
+        saveRDS(data, cache_file)
+
+        data
+    } else {
+        # If the cache file exists, we restore the data from it.
+        readRDS(cache_file)
+    }
+}
+
+#' Merge genome data from files in `path` into `data.table`s.
+#'
+#' The result will be a list with two items:
+#' - `genes` will be a table with one row per unique `geneid` and multiple
+#'   columns per species containing the data of interest. 
+#' - `species` will contain information that is useful to be accessed by
+#'   species.
+#'
+#' @seealso [load_data_cached()]
+load_data <- function(path) {
+    # The resulting table for information by gene. For each species, columns
+    # will be appended.
+    genes_table <- data.table(geneid = integer())
+
+    # The resulting table for information by species. This will result in a
+    # warning, because all median_distance values will be filled with `NA`
+    # (correctly).
+    species_table <- data.table(species, median_distance = numeric())
+
+    file_names <- list.files(path, "*_raw.txt")
+
+    for (file_name in file_names) {
+        species_id <- strsplit(file_name, split = "_")[[1]][1]
+        genes_table_for_species <- fread(paste(path, file_name, sep = "/"))
+
+        # Fill in the new column of the species table (`median_distance`).
+        species_table[
+            id == species_id,
+            median_distance := median(genes_table_for_species[, dist])
+        ]
+
+        # Column names have to be unique for each species.
+        colnames(genes_table_for_species)[c(2, 3, 4)] <- c(
+            paste(species_id, c("dist", "name", "chromosome"), sep = "_")
+        )
+
+        # Add new genes as rows as well as new columns for this species.
+        genes_table <- merge(
+            genes_table,
+            genes_table_for_species,
+            all = TRUE
+        )
+    }
+
+    list(
+        genes = genes_table,
+        species = species_table
+    )
+}