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analyze: Turn analysis into S3 class

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Elias Projahn 2021-11-05 14:33:39 +01:00
parent 55958e0d85
commit 4792bbaefd
1 changed files with 15 additions and 9 deletions
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24
R/analyze.R
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@ -5,9 +5,10 @@
#' function should accept a number between 0.0 and 1.0 for the current #' function should accept a number between 0.0 and 1.0 for the current
#' progress. #' progress.
#' #'
#' @return A [data.table] with one row for each gene identified by it's ID #' @return An object containing the results of the analysis. It contains a
#' (`gene` column). The additional columns contain the resulting scores per #' [data.table] with one row for each gene identified by it's ID (`gene`
#' method and are named after the method IDs. #' column). The additional columns contain the resulting scores per method
#' and are named after the method IDs.
#' #'
#' @export #' @export
analyze <- function(preset, progress = NULL) { analyze <- function(preset, progress = NULL) {
@ -33,10 +34,10 @@ analyze <- function(preset, progress = NULL) {
"neural" = neural "neural" = neural
) )
cached("results", preset, { analysis <- cached("analysis", preset, {
total_progress <- 0.0 total_progress <- 0.0
method_count <- length(preset$method_ids) method_count <- length(preset$methods)
results <- data.table(gene = preset$gene_ids) analysis <- data.table(gene = preset$gene_ids)
for (method_id in preset$methods) { for (method_id in preset$methods) {
method_progress <- if (!is.null(progress)) { method_progress <- if (!is.null(progress)) {
@ -48,8 +49,8 @@ analyze <- function(preset, progress = NULL) {
method_results <- methods[[method_id]](preset, method_progress) method_results <- methods[[method_id]](preset, method_progress)
setnames(method_results, "score", method_id) setnames(method_results, "score", method_id)
results <- merge( analysis <- merge(
results, analysis,
method_results, method_results,
by = "gene" by = "gene"
) )
@ -61,6 +62,11 @@ analyze <- function(preset, progress = NULL) {
progress(1.0) progress(1.0)
} }
results analysis
}) })
structure(
analysis,
class = c("geposan_analysis", class(analysis))
)
} }