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analyze: Include preset in result

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Elias Projahn 2021-11-12 10:16:11 +01:00
parent 6d9511fa2e
commit 910eb06fe9
4 changed files with 32 additions and 21 deletions
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27
R/analyze.R
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@ -5,10 +5,14 @@
#' function should accept a number between 0.0 and 1.0 for the current
#' progress.
#'
#' @return An object containing the results of the analysis. It contains a
#' [data.table] with one row for each gene identified by it's ID (`gene`
#' column). The additional columns contain the resulting scores per method
#' and are named after the method IDs.
#' @returns An object containing the results of the analysis with the following
#' items:
#' \describe{
#' \item{`preset`}{The preset that was used.}
#' \item{`results`}{A [data.table] with one row for each gene identified by
#' it's ID (`gene` column). The additional columns contain the resulting
#' scores per method and are named after the method IDs.}
#' }
#'
#' @export
analyze <- function(preset, progress = NULL) {
@ -34,10 +38,10 @@ analyze <- function(preset, progress = NULL) {
"neural" = neural
)
analysis <- cached("analysis", preset, {
results <- cached("analysis", preset, {
total_progress <- 0.0
method_count <- length(preset$methods)
analysis <- data.table(gene = preset$gene_ids)
results <- data.table(gene = preset$gene_ids)
for (method_id in preset$methods) {
method_progress <- if (!is.null(progress)) {
@ -50,7 +54,7 @@ analyze <- function(preset, progress = NULL) {
setnames(method_results, "score", method_id)
analysis <- merge(
analysis,
results,
method_results,
by = "gene"
)
@ -62,11 +66,14 @@ analyze <- function(preset, progress = NULL) {
progress(1.0)
}
analysis
results
})
structure(
analysis,
class = c("geposan_analysis", class(analysis))
list(
preset = preset,
results = results
),
class = "geposan_analysis"
)
}