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analyze: Include preset in result

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This commit is contained in:
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"
)
}

8
R/ranking.R
View file

@ -7,9 +7,9 @@
#' @param weights Named list pairing method names with weighting factors. Only
#' methods that are contained within this list will be included.
#'
#' @returns A ranking object. The object extends the analysis with additional
#' columns containing the `score` and the `rank` of each gene. It will be
#' ordered by rank.
#' @returns A ranking object. The object extends the analysis result with
#' additional columns containing the `score` and the `rank` of each gene. It
#' will be ordered by rank.
#'
#' @export
ranking <- function(analysis, weights) {
@ -17,7 +17,7 @@ ranking <- function(analysis, weights) {
stop("Invalid analyis. Use geposan::analyze().")
}
ranking <- copy(analysis)
ranking <- copy(analysis$results)
ranking[, score := 0.0]
for (method in names(weights)) {