fix as.vector() - closes issue #203

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: QFeatures
 Title: Quantitative features for mass spectrometry data
-Version: 1.13.2
+Version: 1.13.3
 Authors@R: c(person("Laurent", "Gatto",
                     email = "[email protected]",
                     comment = c(ORCID = "0000-0002-1520-2268"),

NEWS.md

@@ -1,5 +1,9 @@
 # QFeatures 1.13
 
+## QFeatures 1.13.3
+
+- Fix `is.vector()` (see issue #203)
+
 ## QFeatures 1.13.2
 
 - Move the `filterFeatures` generic method to `ProtGenerics`.

R/QFeatures-aggregation.R

@@ -307,11 +307,11 @@ setMethod("aggregateFeatures", "SummarizedExperiment",
     if (!fcol %in% names(rd))
         stop("'fcol' not found in the assay's rowData.")
     groupBy <- rd[[fcol]]
-    
+
     ## Store class of assay i in case it is not a SummarizedExperiment
     ## so that the aggregated assay can be reverted to that class
     .class <- class(object)
-    
+
     ## Message about NA values is quant/row data
     has_na <- character()
     if (anyNA(m))
@@ -326,8 +326,8 @@ setMethod("aggregateFeatures", "SummarizedExperiment",
                      "effects of missing values on data aggregation.")
         message(paste(strwrap(msg), collapse = "\n"))
     }
-    
-    if (is.vector(groupBy)) {
+
+    if (is.vector(groupBy) & !is.list(groupBy)) { ## atomic vectors
         aggregated_assay <- aggregate_by_vector(m, groupBy, fun, ...)
         aggcount_assay <- aggregate_by_vector(m, groupBy, colCounts)
         aggregated_rowdata <- QFeatures::reduceDataFrame(rd, rd[[fcol]],
@@ -348,14 +348,14 @@ setMethod("aggregateFeatures", "SummarizedExperiment",
         ## Count the number of peptides per protein
         .n <- apply(groupBy != 0, 2, sum)
         aggregated_rowdata[[".n"]] <- .n[rownames(aggregated_rowdata)]
-        
+
         assays <- SimpleList(assay = as.matrix(aggregated_assay)) ## to discuss
         rowdata <- aggregated_rowdata[rownames(aggregated_assay), , drop = FALSE]
     } else stop("'fcol' must refer to a vector or a sparse matrix.")
     se <- SummarizedExperiment(assays = assays,
                                colData = colData(object),
                                rowData = rowdata)
-    
+
     ## If the input objects weren't SummarizedExperiments, then try to
     ## convert the merged assay into that class. If the conversion
     ## fails, keep the SummarizedExperiment, otherwise use the