correct assay call due to changes in SummarizedExperiment and the fol…

…lowing commit Bioconductor/SummarizedExperiment@495ab00

R/class-OutriderDataSet.R

@@ -210,8 +210,8 @@ makeExampleOutriderDataSet <- function(n=200, m=80, q=10, freq=1E-3, zScore=6,
     colnames(countData) <- paste0("sample_", seq_len(m))
     ods <- OutriderDataSet(countData=countData)
 
-    assay(ods, "trueMean")            <- mu
-    assay(ods, "trueSd")              <- matrix(true_sd, nrow=n, ncol=m)
+    assay(ods, "trueMean", withDimnames=FALSE) <- mu
+    assay(ods, "trueSd", withDimnames=FALSE) <- matrix(true_sd, nrow=n, ncol=m)
     mcols(ods)[,"trueTheta"]          <- theta
     colData(ods)[['trueSizeFactor']]  <- sf
     metadata(ods)[['optimalEncDim']]  <- q
@@ -254,9 +254,9 @@ makeExampleOutriderDataSet <- function(n=200, m=80, q=10, freq=1E-3, zScore=6,
     }
     mode(k) <- "integer"
 
-    assay(ods, 'trueCounts') <- counts(ods)
-    counts(ods) <- k
-    assay(ods, "trueOutliers") <- indexOut
+    assay(ods, 'trueCounts', withDimnames=FALSE) <- counts(ods)
+    counts(ods, withDimnames=FALSE) <- k
+    assay(ods, "trueOutliers", withDimnames=FALSE) <- indexOut
 
     return(ods)
 }

R/getNSetterFuns.R

@@ -4,7 +4,7 @@
 #' the values within the OUTRIDER model.
 #' 
 #' @param ods,object An OutriderDataSet object.
-#' @param ... Further arguments currently not in use.
+#' @param ... Further arguments passed on to the underlying assay function.
 #' @return A matrix or vector dependent on the type of data retrieved.
 #' 
 #' @name getter_setter_functions
@@ -33,10 +33,10 @@ zScore <- function(ods){
     assay(ods, 'zScore')
 }
 
-`zScore<-` <- function(ods, value){
+`zScore<-` <- function(ods, ..., value){
     stopifnot(is.matrix(value))
     stopifnot(dim(ods) == dim(value))
-    assay(ods, 'zScore') <- value
+    assay(ods, 'zScore', ...) <- value
     return(ods)
 }
 
@@ -49,10 +49,10 @@ pValue <- function(ods){
     assay(ods, 'pValue')
 }
 
-`pValue<-` <- function(ods, value){
+`pValue<-` <- function(ods, ..., value){
     stopifnot(is.matrix(value))
     stopifnot(dim(ods) == dim(value))
-    assay(ods, 'pValue') <- value
+    assay(ods, 'pValue', ...) <- value
     return(ods)
 }
 
@@ -66,10 +66,10 @@ padj <- function(ods){
     assay(ods, 'padjust')
 }
 
-`padj<-` <- function(ods, value){
+`padj<-` <- function(ods, ..., value){
     stopifnot(is.matrix(value))
     stopifnot(dim(ods) == dim(value))
-    assay(ods, 'padjust') <- value
+    assay(ods, 'padjust', ...) <- value
     return(ods)
 }
 

R/method-counts.R

@@ -1,7 +1,7 @@
 
-counts.replace.OutriderDataSet <- function(object, value){
+counts.replace.OutriderDataSet <- function(object, ..., value){
     mode(value) <- "integer"
-    assays(object)[["counts"]] <- value
+    assay(object, "counts", ...) <- value
 
     validObject(object)
     object
@@ -53,6 +53,7 @@ counts.OutriderDataSet <- function(object, normalized=FALSE, minE=0.5){
 #' @param normalized TRUE/FALSE whether counts should be normalized
 #' @param value An integer matrix containing the counts
 #' @param minE minimal expected count.
+#' @param ... Further arguments are passed on to the underlying assay function
 #' @return A matrix containing the counts
 #' 
 #' @seealso \code{\link{sizeFactors}}, \code{\link{normalizationFactors}}

R/method-gridSearch.R

@@ -207,9 +207,10 @@ injectOutliers <- function(ods, freq, zScore, inj, lnorm, sdlog){
         }
     }
     # save coruppted counts and index of corruption into ods
-    assay(ods, 'counts') <- matrix(as.integer(counts),nrow(ods))
-    assay(ods, 'trueCorruptions') <- index
-    assay(ods, 'injectedZscore') <- zScore
+    assay(ods, 'counts', withDimnames=FALSE) <- matrix(as.integer(counts), 
+            nrow=nrow(ods))
+    assay(ods, 'trueCorruptions', withDimnames=FALSE) <- index
+    assay(ods, 'injectedZscore', withDimnames=FALSE) <- zScore
     return(ods)
 }
 

R/pValMatrix.R

@@ -74,8 +74,8 @@ pValMatrix <- function(ods, alternative, BPPARAM){
     pValMat <- bplapply(seq_along(ods), pVal, ctsData=ctsData, theta=thetaMat,
             mu=mu, normF=normF, alternative=alternative, BPPARAM=BPPARAM)
 
-    pValMat <- 
-    pValue(ods) <- matrix(unlist(pValMat), nrow=length(ods), byrow=TRUE)
+    pValue(ods) <- matrix(unlist(pValMat), nrow=length(ods), 
+            byrow=TRUE, dimnames=dimnames(ods))
     validObject(ods)
     return(ods)
 }

tests/testthat/helper_test_data_set.R

@@ -71,9 +71,9 @@ get_test_outrider_dataset <- function(){
     normalizationFactors(ods) <- normF_round3
     mcols(ods)[['mu']] <- mu_round4
     mcols(ods)[['disp']] <- disp_round4
-    assays(ods)[['pValue']] <- pval_round4
-    assays(ods)[['padjust']] <- padj_round4
-    assays(ods)[['zScore']] <- zscore_round4
+    assay(ods, 'pValue', withDimnames=FALSE)  <- pval_round4
+    assay(ods, 'padjust', withDimnames=FALSE) <- padj_round4
+    assay(ods, 'zScore', withDimnames=FALSE)  <- zscore_round4
 
     return(ods)
 }

tests/testthat/test_helper.R

@@ -9,10 +9,12 @@ test_that("check ODS object", {
     ods <- estimateSizeFactors(ods)
 
     expect_error(checkFullAnalysis(ods), "Please calculate the P-values before")
-    padj(ods) <- matrix(runif(ncol(ods)*nrow(ods)), ncol=ncol(ods))
+    padj(ods) <- matrix(runif(ncol(ods)*nrow(ods)), 
+            ncol=ncol(ods), dimnames=dimnames(ods))
 
     expect_error(checkFullAnalysis(ods), "Please calculate the Z-scores before")
-    zScore(ods) <- matrix(runif(ncol(ods)*nrow(ods)), ncol=ncol(ods))
+    zScore(ods) <- matrix(runif(ncol(ods)*nrow(ods)), 
+            ncol=ncol(ods), dimnames=dimnames(ods))
 
     expect_true(checkFullAnalysis(ods))
 })

tests/testthat/test_methods.R

@@ -37,7 +37,7 @@ test_that("result method", {
 
 test_that("normalization method", {
     ods <- makeExampleOutriderDataSet(5, 5)
-    counts(ods) <- matrix(1:5, ncol=5, nrow=5)
+    counts(ods) <- matrix(1:5, ncol=5, nrow=5, dimnames=dimnames(ods))
     expect_null(normalizationFactors(ods))
     nMat <- matrix(6:10, ncol=5, nrow=5)
     normalizationFactors(ods) <- nMat