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Adding new function selectNoReplicateOrganoids(); refactoring code; update documentation
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-162
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‎NAMESPACE

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@@ -2,10 +2,12 @@
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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(getClassNoReplicateOneDrug)
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export(getClassOneDrug)
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export(plotDrugAUCDensityCurve)
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export(plotDrugAUCViolinPlot)
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export(selectOrgForOneDrug)
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export(selectOrgWithoutReplicateForOneDrug)
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export(selectNoReplicateOrganoids)
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importFrom(S4Vectors,isSingleNumber)
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importFrom(ggplot2,.data)
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importFrom(ggplot2,aes)
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importFrom(ggridges,geom_density_ridges)
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importFrom(ggridges,position_points_jitter)
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importFrom(methods,is)
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importFrom(stats,fisher.test)
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importFrom(stats,quantile)

‎R/OrganoidsToolBox.R

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#'
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#' @seealso
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#' \itemize{
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#' \item \code{\link{selectOrgForOneDrug}} {for selecting the organoids
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#' \item \code{\link{getClassOneDrug}} {for selecting the organoids
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#' with sensitive and resistant behavior for a specific drug screening.}
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#' }
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#' @encoding UTF-8
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#'
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#' @seealso
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#' \itemize{
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#' \item \code{\link{selectOrgForOneDrug}} { for selecting the organoids
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#' \item \code{\link{getClassOneDrug}} { for selecting the organoids
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#' with sensitive and resistant behavior for a
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#' specific drug screening.}
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#' }
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#'
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#' ## Calculate the extreme organoids for the methotrexate drug screening
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#' ## using a quantile of 1/3
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#' results <- selectOrgForOneDrug(drugScreening=simpleDrugScreening,
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#' results <- getClassOneDrug(drugScreening=simpleDrugScreening,
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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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#'
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#' @seealso
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#' \itemize{
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#' \item \code{\link{selectOrgForOneDrug}} { for selecting the organoids
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#' \item \code{\link{getClassOneDrug}} { for selecting the organoids
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#' with sensitive and resistant behavior for a
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#' specific drug screening.}
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#' }
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#'
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#' ## Calculate the extreme organoids for the methotrexate drug screening
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#' ## using a quantile of 1/3
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#' results <- selectOrgForOneDrug(drugScreening=drugScreening,
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#' results <- getClassOneDrug(drugScreening=drugScreening,
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#' drugName="Methotrexate", study="MEGA-TEST", screenType="TEST-01",
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#' doseType="Averaged", quantile=1/4)
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#'
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#'
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#' @seealso
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#' \itemize{
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#' \item \code{\link{selectOrgForOneDrug}} { for selecting the organoids
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#' \item \code{\link{getClassOneDrug}} { for selecting the samples
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#' with sensitive and resistant behavior for a
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#' specific drug screening.}
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#' \item \code{\link{selectOrgWithoutReplicateForOneDrug}} { for selecting
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#' the unrelated organoids (only one organoid per patient)
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#' \item \code{\link{getClassNoReplicateOneDrug}} { for selecting
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#' the unrelated samples (only one sample per patient)
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#' with sensitive and resistant behavior for a
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#' specific drug screening.}
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#' }
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#'
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#' ## Calculate the extreme organoids for the methotrexate drug screening
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#' ## using a quantile of 1/3
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#' results <- selectOrgWithoutReplicateForOneDrug(drugScreening=drugScreening,
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#' results <- getClassNoReplicateOneDrug(drugScreening=drugScreening,
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#' drugName="Methotrexate", study="MEGA-TEST", screenType="TEST-01",
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#' patientInfo=patientInfo, doseType="Averaged", quantile=1/4)
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#'

‎R/drugScreening-internal.R

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#' @param drugName a single \code{character} string representing the
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#' selected drug.
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#'
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#' @param study a single \code{character} string representing the name of
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#' @param study a \code{vector} of \code{character} string representing the
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#' name(s) of
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#' the study selected for the analyses. The study must be present in the drug
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#' screening dataset. The study can be found in the 'study' column of the
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#' drug screening dataset.
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doseType) {
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## Select the specified study
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selectedDrug <- drugData[which(tolower(drugData$study) ==
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selectedDrug <- drugData[which(tolower(drugData$study) %in%
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tolower(study)), ]
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## Select the specified screen type
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#' @param drugName a single \code{character} string representing the name of
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#' the drug selected for the analyses.
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#'
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#' @param study a single \code{character} string representing the name of
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#' the study selected for the analyses.
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#' @param study a \code{vector} of \code{character} string representing
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#' the name of the study selected for the analyses.
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#'
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#' @param screenType a \code{vector} of \code{character} string representing
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#' the type of
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#' screening selected for the analyses.
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#' @title Validate input parameters for the
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#' selectOrgWithoutReplicateForOneDrug() function
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#' getClassNoReplicateOneDrug() function
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#'
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#' @description The function validates the input parameters for the
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#' selectOrgWithoutReplicateForOneDrug() function.
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#' getClassNoReplicateOneDrug() function.
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#'
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#' @param drugScreening a single \code{character} string representing the path
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#' and name of the drug screening file that contains the information needed
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#' @importFrom S4Vectors isSingleNumber
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#' @encoding UTF-8
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#' @keywords internal
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validateSelectOrgWithoutReplicateForOneDrug<- function(drugScreening,
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validateSelectOrgWithoutReplicateForOneDrug <- function(drugScreening,
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drugName, study, screenType, patientInfo, doseType, quantile) {
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## Validate all but patientInfo parameter
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return(0L)
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}
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#' @title Validate input parameters for the
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#' selectNoReplicateOrganoids() function
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#'
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#' @description The function validates the input parameters for the
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#' selectNoReplicateOrganoids() function.
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#'
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#' @param drugScreening a \code{data.frame} containing the drug screening
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#' information. The 'organoid_id' column is mandatory.
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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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#' @return the value \code{0L} when successful.
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#'
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#' @examples
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#'
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#' ## Load drug screen dataset for 1 drug
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#' data(drugScreening)
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#'
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#' ## Load patient information dataset
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#' data(patientInfo)
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#'
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#' ## Validation should return OL as all parameters are valids
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#' OrganoidsToolBox:::validateSelectNoReplicateOrganoids(
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#' drugScreening=drugScreening, patientInfo=patientInfo)
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#'
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#' @author Astrid Deschênes, Pascal Belleau
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#' @importFrom S4Vectors isSingleNumber
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#' @encoding UTF-8
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#' @keywords internal
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validateSelectNoReplicateOrganoids <- function(drugScreening,patientInfo) {
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if (!is.data.frame(drugScreening)) {
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stop("The \'drugScreening\' must be a data.frame.")
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}
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## Check for mandatory columns in drugScreening
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if (!('organoid_id' %in% colnames(drugScreening))) {
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stop("The mandatory column \'organoid_id\' is missing.")
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}
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if (!is.data.frame(patientInfo)) {
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stop("The \'patientInfo\' must be a data.frame.")
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}
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## Check for mandatory columns in patientInfo
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if (!all(c('organoid_id', 'patient_id') %in% colnames(patientInfo))) {
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stop("Mandatory columns are missing from the patient info ",
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"dataset. The mandatory columns are: \'organoid_id\' and ",
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"\'patient_id\'.")
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}
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return(0L)
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}
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