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Add fisherCategoricalVariable() function
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‎NAMESPACE

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# Generated by roxygen2: do not edit by hand
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S3method(is,DrugAUCQuantile)
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S3method(is,DrugAUCQuantileNoReplicate)
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export(fisherCategoricalVariable)
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export(getClassOneDrug)
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export(plotDrugAUCDensityCurve)

‎R/AllGenerics.R

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is.DrugAUCQuantile <- function(x, ...) {
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inherits(x, "DrugAUCQuantile")
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}
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#' @title Is an object of class \code{DrugAUCQuantileNoReplicate}
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#'
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#' @description Functions to test inheritance relationships between an
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#' object and class \code{DrugAUCQuantileNoReplicate}.
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#'
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#' @method is DrugAUCQuantileNoReplicate
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#'
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#' @param x an object.
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#'
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#' @param \ldots further arguments passed to or from other methods.
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#'
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#' @return a \code{logical}.
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#'
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#' @importFrom methods is
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#' @export
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is.DrugAUCQuantileNoReplicate <- function(x, ...) {
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inherits(x, "DrugAUCQuantileNoReplicate")
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}

‎R/drugScreening.R

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@@ -184,8 +184,7 @@ selectNoReplicateOrganoids <- function(drugScreening, patientInfo) {
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#' returns a "\code{ggplot}" object. The density plot can be split by
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#' sensitivity classes.
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#'
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#' @param drugQuantile an object of class "\code{DrugAUCQuantile}" or
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#' "\code{DrugAUCQuantileNoReplicate}" which
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#' @param drugQuantile an object of class "\code{DrugAUCQuantile}" which
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#' contains the sensitive and resistant information for organoids associated
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#' to a specific drug screening.
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#'
@@ -220,10 +219,9 @@ selectNoReplicateOrganoids <- function(drugScreening, patientInfo) {
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plotDrugAUCDensityCurve <- function(drugQuantile, byGroup=FALSE) {
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## Validate that the drugQuantile parameter is a DrugAUCQuantile object
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if (!(is.DrugAUCQuantile(drugQuantile) ||
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is.DrugAUCQuantileNoReplicate(drugQuantile))) {
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stop("The \'drugQuantile\' parameter must be a DrugAUCQuantile or ",
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"DrugAUCQuantileNoReplicate object.")
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if (!(is.DrugAUCQuantile(drugQuantile))) {
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stop("The \'drugQuantile\' parameter must be a DrugAUCQuantile ",
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"object.")
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}
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## Validate that the byGroup is logical
@@ -333,10 +331,9 @@ plotDrugAUCDensityCurve <- function(drugQuantile, byGroup=FALSE) {
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plotDrugAUCViolinPlot <- function(drugQuantile, min=0, max=100, trim=FALSE) {
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## Validate that the drugQuantile parameter is a DrugAUCQuantile object
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if (!(is.DrugAUCQuantile(drugQuantile) ||
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is.DrugAUCQuantileNoReplicate(drugQuantile))) {
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stop("The \'drugQuantile\' parameter must be a DrugAUCQuantile or ",
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"DrugAUCQuantileNoReplicate object.")
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if (!(is.DrugAUCQuantile(drugQuantile))) {
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stop("The \'drugQuantile\' parameter must be a DrugAUCQuantile",
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" object.")
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}
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## Validate that the min is a single numeric

‎R/enrichment.R

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#' @param drugQuantile an object of class "\code{DrugAUCQuantile}" which
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#' contains the sensitive and resistant organoids for a specific drug.
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#'
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#' @param patientInfo a \code{data.frame} containing the meta-data information
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#' related to the organoids. The mandatory columns are: 'organoid_id'
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#' and 'patient_id'.
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#'
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#' @param category a single \code{character} string representing the column
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#' from the 'patientInfo' dataset that should be used as the
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#' from the "\code{DrugAUCQuantile}" extreme dataset that should be used as the
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#' categorical variable.
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#'
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#' @return a \code{list} containing 2 components:
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#' drugName="Methotrexate", study="MEGA-TEST", screenType="TEST-01",
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#' doseType="Averaged", quantile=1/3)
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#'
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#' ## The classification of the organoids is in the 'extreme' entry
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#' ## TODO
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#' results$extreme
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#'
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#' @author Astrid Deschênes, Pascal Belleau
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#' @importFrom stats fisher.test
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#' @encoding UTF-8
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#' @export
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fisherCategoricalVariable <- function(drugQuantile, patientInfo, category) {
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fisherCategoricalVariable <- function(drugQuantile, category) {
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## Validate that the drugQuantile parameter is a DrugAUCQuantile object
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if (!(is.DrugAUCQuantile(drugQuantile) ||
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is.DrugAUCQuantileNoReplicate(drugQuantile))) {
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if (!(is.DrugAUCQuantile(drugQuantile))) {
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stop("The \'drugQuantile\' parameter must be a DrugAUCQuantile ",
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"object.")
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}
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if (!is.data.frame(patientInfo)) {
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stop("The \'patientInfo\' parameter must be a data.frame.")
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}
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if (!is.character(category)) {
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stop("The \'category\' parameter must be a character string.")
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}
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## The drug must be present in the drug dataset
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if (!(category %in% colnames(patientInfo))) {
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if (!(category %in% colnames(drugQuantile$extreme))) {
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stop("The category \'", category, "\' must be one of the columns in ",
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"the \'patientInfo\' dataset.")
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"the \'DrugAUCQuantile\' dataset.")
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}
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results <- drugQuantile$extreme
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resultsD <- merge(results, patientInfo[, c("organoid_id", category)],
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by="organoid_id", all.x = TRUE)
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sensitive <- resultsD[resultsD$group == "SENSITIVE",]
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resistant <- resultsD[resultsD$group == "RESISTANT",]
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sensitive <- results[results$group == "SENSITIVE",]
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resistant <- results[results$group == "RESISTANT",]
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categoryAll <- unique(resultsD[[category]])
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categoryAll <- unique(results[[category]])
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all <- list()
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for (i in categoryAll) {

‎man/fisherCategoricalVariable.Rd

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‎man/is.DrugAUCQuantileNoReplicate.Rd

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‎man/plotDrugAUCDensityCurve.Rd

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‎tests/testthat/test-drugScreening.R

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@@ -291,7 +291,7 @@ context("plotDrugAUCViolinPlot() results")
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test_that("plotDrugAUCViolinPlot() must return error when drugQuantile is character string", {
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error_message <- paste0("The \'drugQuantile\' parameter must ",
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"be a DrugAUCQuantile or DrugAUCQuantileNoReplicate object.")
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"be a DrugAUCQuantile object.")
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expect_error(plotDrugAUCViolinPlot(drugQuantile="test", min=0, max=100,
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trim=FALSE), error_message, fixed=TRUE)
@@ -353,7 +353,7 @@ context("plotDrugAUCViolinPlot() results")
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test_that("plotDrugAUCDensityCurve() must return error when drugQuantile is character string", {
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error_message <- paste0("The \'drugQuantile\' parameter must be a ",
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"DrugAUCQuantile or DrugAUCQuantileNoReplicate object.")
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"DrugAUCQuantile object.")
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expect_error(plotDrugAUCDensityCurve(drugQuantile="33", byGroup=FALSE),
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error_message, fixed=TRUE)

‎tests/testthat/test-enrichment.R

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@@ -13,14 +13,25 @@ context("fisherCategoricalVariable() results")
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test_that("fisherCategoricalVariable() must return error when drugQuantile is numeric", {
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patientData <- data.frame(organoid_id=c("hT1001", "hT1082", "hT1919",
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"hT3312", "hT1051", "hT2211", "hT2212", "hT2213", "hT2251"),
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patient_id=c("1", "2", "3", "2", "3", "4", "4", "6", "7"),
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stringsAsFactors=FALSE)
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error_message <- paste0("The \'drugQuantile\' parameter must be a ",
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"DrugAUCQuantile object.")
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expect_error(fisherCategoricalVariable(drugQuantile=33,
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patientInfo=patientData, category="test"), error_message, fixed=TRUE)
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expect_error(fisherCategoricalVariable(drugQuantile=33, category="test"),
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error_message, fixed=TRUE)
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})
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test_that("fisherCategoricalVariable() must return error when category is numeric", {
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drug <- readRDS(test_path("fixtures", "OneDrugDemoFile02.RDS"))
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results <- getClassOneDrug(drugScreening=drug, drugName="Methotrexate",
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study="MEGA-TEST", screenType="TEST-01", doseType="Averaged",
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quantile=0.2)
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error_message <- paste0("The \'category\' parameter must be a character",
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" string.")
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expect_error(fisherCategoricalVariable(drugQuantile=results,
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category=22), error_message, fixed=TRUE)
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})

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