BUG FIX: poolRuns() would produce an error [#112]

ccagc · Jul 23, 2024 · 99da9f8 · 99da9f8
1 parent 2c45bf9
commit 99da9f8
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: QDNAseq
-Version: 1.41.1-9000
+Version: 1.41.1-9001
 Title: Quantitative DNA Sequencing for Chromosomal Aberrations
 Depends: R (>= 3.1.0)
 Imports:

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,10 @@
 # Version (development version)
 
- * ...
+## Bug Fixes
+
+ * `poolRuns()` would give an error "Error in colMeans2(oldphenodata,
+   cols = numericCols, useNames = FALSE) : Argument 'x' must be a
+   matrix or a vector."
 
 
 # Version 1.41.1 [2024-07-20]

diff --git a/R/poolRuns.R b/R/poolRuns.R
@@ -94,19 +94,18 @@ setMethod("poolRuns", signature=c(object="QDNAseqSignals",
         totalReads <- sum(oldphenodata$total.reads)
         usedReads <- sum(oldphenodata$used.reads)
         numericCols <- sapply(oldphenodata, FUN=is.numeric)
-        oldphenodata[1, numericCols] <- colMeans2(oldphenodata, cols=numericCols, useNames=FALSE)
-        oldphenodata[1, !numericCols] <- apply(oldphenodata[, !numericCols,
-            drop=FALSE], MARGIN=2L, concatenateIfNotEqual)
+        oldphenodata[1,  numericCols] <- apply(oldphenodata[,  numericCols, drop = FALSE], MARGIN = 2L, FUN = mean)
+        oldphenodata[1, !numericCols] <- apply(oldphenodata[, !numericCols, drop = FALSE], MARGIN = 2L, FUN = concatenateIfNotEqual)
         if ("paired.ends" %in% colnames(oldphenodata))
             oldphenodata[1, "paired.ends"] <- pairedEnds
         oldphenodata[1, "total.reads"] <- totalReads
         oldphenodata[1, "used.reads"] <- usedReads
         newphenodata <- rbind(newphenodata, oldphenodata[1, ], stringsAsFactors=FALSE)
     }
-    rownames(newphenodata) <- newphenodata[, 1]
-    newphenodata <- AnnotatedDataFrame(newphenodata,
-        varMetadata=varMetadata(object))
-
+    rownames(newphenodata) <- newphenodata$name
+    metadata <- varMetadata(object)
+    metadata <- rbind(metadata, structure(data.frame(labelDescription = NA_character_), rownames = "total.reads"))
+    newphenodata <- AnnotatedDataFrame(newphenodata, varMetadata=metadata)
     if (inherits(object, "QDNAseqReadCounts")) {
         storage.mode(newcounts) <- "integer"
         object2 <- new("QDNAseqReadCounts",

diff --git a/tests/poolRuns.R b/tests/poolRuns.R
@@ -25,11 +25,9 @@ message("poolRuns(LGG150set) ...")
 x_pool <- poolRuns(x, samples = sampleNames(x))
 print(x_pool)
 
-if (FALSE) {
 message("poolRuns(LGG150set) - pooled ...")
 ## BUG #112 (https://github.com/ccagc/QDNAseq/issues/112)
 x_pool <- poolRuns(x, samples = rep("pooled", times = 2L))
 print(x_pool)
-}
 
 message("poolRuns(LGG150set) ... done")