@@ -22,7 +22,6 @@ S3method(print,COMPASSResult)

 S3method(subset,COMPASSContainer)

 S3method(summary,COMPASSContainer)

 S3method(summary,COMPASSResult)

-export(">=")

 export("COMPASSDescription<-")

 export("metadata<-")

 export(COMPASS)

@@ -45,12 +44,9 @@ export(SimpleCOMPASS)

 export(TotalCellCounts)

 export(UniqueCombinations)

 export(categories)

-export(condition)

-export(degree)

 export(getCounts)

 export(markers)

 export(metadata)

-export(on)

 export(pheatmap)

 export(plot2)

 export(plotCOMPASSResultStack)

@@ -60,7 +56,6 @@ export(shinyCOMPASS)

 export(shinyCOMPASSDeps)

 export(translate_marker_names)

 export(transpose_list)

-export(x)

 import(data.table)

 import(grid)

 import(magrittr)

@@ -14,16 +14,15 @@

 #' @details

 #' The response is computed from the sampled Gamma matrix, subsetting on the selected markers, and

 #' @return  A \code{vector} of response probabilities for each subject.

-#' @export

-#'

 #' @examples

+#'

 #' Response(CR, markers = c("M1","M2","M3"), degree = 2)

+#' @export

 Response <- function(x, markers, degree, max.prob, cond_response){

   UseMethod("Response")

 }

 ##' @rdname Response

-##' @export

 Response.COMPASSResult <- function(x, markers = NULL, degree = 1, max.prob = FALSE, cond_response = FALSE) {

   ## we drop the last column as it is the 'NULL' category

   if (is.null(markers)) {

@@ -63,7 +62,7 @@ Response.COMPASSResult <- function(x, markers = NULL, degree = 1, max.prob = FAL

       rownames(response) <- rownames(new_mean_gamma)

       colnames(response) <- paste0("Pr(response|degree >=",degree,")")

     }else{

-      #' condition on degree >= x

+      #condition on degree >= x

       response <- new_mean_gamma[,include_cols, drop = FALSE]

       if (!max.prob & !cond_response) {

         # probability of response from total probability

@@ -34,5 +34,6 @@ i.e., the probability of at least \code{degree} markers exhibiting an antigen sp

 The response is computed from the sampled Gamma matrix, subsetting on the selected markers, and

 }

 \examples{

+

 Response(CR, markers = c("M1","M2","M3"), degree = 2)

 }