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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
View file

@ -5,10 +5,14 @@
#' 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 An object containing the results of the analysis. It contains a #' @returns An object containing the results of the analysis with the following
#' [data.table] with one row for each gene identified by it's ID (`gene` #' items:
#' column). The additional columns contain the resulting scores per method #' \describe{
#' and are named after the method IDs. #' \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 #' @export
analyze <- function(preset, progress = NULL) { analyze <- function(preset, progress = NULL) {
@ -34,10 +38,10 @@ analyze <- function(preset, progress = NULL) {
"neural" = neural "neural" = neural
) )
analysis <- cached("analysis", preset, { results <- cached("analysis", preset, {
total_progress <- 0.0 total_progress <- 0.0
method_count <- length(preset$methods) method_count <- length(preset$methods)
analysis <- data.table(gene = preset$gene_ids) results <- data.table(gene = preset$gene_ids)
for (method_id in preset$methods) { for (method_id in preset$methods) {
method_progress <- if (!is.null(progress)) { method_progress <- if (!is.null(progress)) {
@ -50,7 +54,7 @@ analyze <- function(preset, progress = NULL) {
setnames(method_results, "score", method_id) setnames(method_results, "score", method_id)
analysis <- merge( analysis <- merge(
analysis, results,
method_results, method_results,
by = "gene" by = "gene"
) )
@ -62,11 +66,14 @@ analyze <- function(preset, progress = NULL) {
progress(1.0) progress(1.0)
} }
analysis results
}) })
structure( structure(
analysis, list(
class = c("geposan_analysis", class(analysis)) 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 #' @param weights Named list pairing method names with weighting factors. Only
#' methods that are contained within this list will be included. #' methods that are contained within this list will be included.
#' #'
#' @returns A ranking object. The object extends the analysis with additional #' @returns A ranking object. The object extends the analysis result with
#' columns containing the `score` and the `rank` of each gene. It will be #' additional columns containing the `score` and the `rank` of each gene. It
#' ordered by rank. #' will be ordered by rank.
#' #'
#' @export #' @export
ranking <- function(analysis, weights) { ranking <- function(analysis, weights) {
@ -17,7 +17,7 @@ ranking <- function(analysis, weights) {
stop("Invalid analyis. Use geposan::analyze().") stop("Invalid analyis. Use geposan::analyze().")
} }
ranking <- copy(analysis) ranking <- copy(analysis$results)
ranking[, score := 0.0] ranking[, score := 0.0]
for (method in names(weights)) { for (method in names(weights)) {

12
man/analyze.Rd
View file

@ -14,10 +14,14 @@ function should accept a number between 0.0 and 1.0 for the current
progress.} progress.}
} }
\value{ \value{
An object containing the results of the analysis. It contains a An object containing the results of the analysis with the following
\link{data.table} with one row for each gene identified by it's ID (\code{gene} items:
column). The additional columns contain the resulting scores per method \describe{
and are named after the method IDs. \item{\code{preset}}{The preset that was used.}
\item{\code{results}}{A \link{data.table} with one row for each gene identified by
it's ID (\code{gene} column). The additional columns contain the resulting
scores per method and are named after the method IDs.}
}
} }
\description{ \description{
Analyze by applying the specified preset. Analyze by applying the specified preset.

6
man/ranking.Rd
View file

@ -13,9 +13,9 @@ ranking(analysis, weights)
methods that are contained within this list will be included.} methods that are contained within this list will be included.}
} }
\value{ \value{
A ranking object. The object extends the analysis with additional A ranking object. The object extends the analysis result with
columns containing the \code{score} and the \code{rank} of each gene. It will be additional columns containing the \code{score} and the \code{rank} of each gene. It
ordered by rank. will be ordered by rank.
} }
\description{ \description{
This function takes the result of \code{\link[=analyze]{analyze()}} and creates a score by This function takes the result of \code{\link[=analyze]{analyze()}} and creates a score by