Merge branch 'master' of git.bioconductor.org:packages/OUTRIDER

# Conflicts: # DESCRIPTION # R/class-OutriderDataSet.R # R/getNSetterFuns.R # R/method-counts.R # R/method-gridSearch.R # tests/testthat/helper_test_data_set.R
gagneurlab · Apr 12, 2020 · 7fbdaaf · 7fbdaaf
2 parents 042e935 + 025e423
commit 7fbdaaf
Show file tree

Hide file tree

Showing 6 changed files with 12 additions and 12 deletions.
diff --git a/R/ZscoreMatrix.R b/R/ZscoreMatrix.R
@@ -59,7 +59,7 @@ ZscoreMatrix <- function(ods, peerResiduals){
         Zscore <- (residuals - rowMeans(residuals)) / rowSds(residuals)
     }
 
-    assay(ods, "l2fc") <- log2fc
+    assay(ods, "l2fc", withDimnames=FALSE) <- log2fc
     zScore(ods) <- Zscore
     validObject(ods)
     return(ods)

diff --git a/R/class-OutriderDataSet.R b/R/class-OutriderDataSet.R
@@ -212,10 +212,10 @@ makeExampleOutriderDataSet <- function(n=200, m=80, q=10, freq=1E-3, zScore=6,
 
     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
-    metadata(ods)[['encDimTable']]    <- data.table(
+    mcols(ods)[,"trueTheta"]                 <- theta
+    colData(ods)[['trueSizeFactor']]         <- sf
+    metadata(ods)[['optimalEncDim']]         <- q
+    metadata(ods)[['encDimTable']]           <- data.table(
         encodingDimension=q, evaluationLoss=1, evalMethod='simulation')
 
     #

diff --git a/R/filterExpression.R b/R/filterExpression.R
@@ -65,7 +65,7 @@ filterExp <- function(ods, fpkmCutoff, percentile, filterGenes, savefpkm,
                     addExpressedGenes){
     fpkm <- fpkm(ods)
     if(savefpkm){
-        assays(ods)[['fpkm']] <- fpkm
+        assay(ods, 'fpkm', withDimnames=FALSE) <- fpkm
     }
     passed <- rowQuantiles(fpkm, probs=percentile) > fpkmCutoff
     mcols(ods)['passedFilter'] <- passed

diff --git a/R/getNSetterFunsInternal.R b/R/getNSetterFunsInternal.R
@@ -116,7 +116,7 @@ trueCounts <- function(ods){
 
 `trueCounts<-` <- function(ods, value){
     if(!'replacedTrueCounts' %in% assayNames(ods)){
-        assay(ods, 'replacedTrueCounts') <- value
+        assay(ods, 'replacedTrueCounts', withDimnames=FALSE) <- value
     }
     return(ods)
 }

diff --git a/R/method-counts.R b/R/method-counts.R
@@ -2,7 +2,7 @@
 counts.replace.OutriderDataSet <- function(object, ..., value){
     mode(value) <- "integer"
     assay(object, "counts", ...) <- value
-    
+
     validObject(object)
     object
 }
@@ -80,7 +80,7 @@ normalizationFactors.OutriderDataSet <- function(object) {
     if (!"normalizationFactors" %in% assayNames(object)){
         return(NULL)
     }
-    assays(object)[["normalizationFactors"]]
+    assay(object, "normalizationFactors")
 }
 
 normFactors.replace.OutriderDataSet <- function(object, value) {
@@ -96,7 +96,7 @@ normFactors.replace.OutriderDataSet <- function(object, value) {
     stopifnot(all(value > 0))
 
     # set the values and check the object
-    assays(object)[["normalizationFactors"]] <- value
+    assay(object, "normalizationFactors", withDimnames=FALSE) <- value
     validObject(object)
     object
 }
@@ -169,6 +169,6 @@ setReplaceMethod("normalizationFactors", signature(object="OutriderDataSet",
 #' @export "normalizationFactors<-"
 setReplaceMethod("normalizationFactors", signature(object="OutriderDataSet", 
         value="NULL"), function(object, value) {
-                assays(object)[["normalizationFactors"]] <- NULL
+                assay(object, "normalizationFactors") <- NULL
                 return(object)})
 
diff --git a/R/method-gridSearch.R b/R/method-gridSearch.R
@@ -156,7 +156,7 @@ findInjectZscore <- function(ods, freq=1E-2,
 #' @noRd
 injectOutliers <- function(ods, freq, zScore, inj, lnorm, sdlog){
     # copy true counts to be able to acces them in the loss later
-    assays(ods)[['trueCounts']] <- counts(ods)
+    assay(ods, 'trueCounts', withDimnames=FALSE) <- counts(ods)
 
     # generate index of injected counts
     size <- prod(dim(ods))