Replace deprecated ecol argument

fmicompbio · Jul 21, 2024 · 4077dac · 4077dac
1 parent e6988c7
commit 4077dac
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -41,7 +41,7 @@ Imports:
     MsCoreUtils,
     msigdbr,
     plotly,
-    QFeatures,
+    QFeatures (>= 1.14.0),
     readr,
     rlang,
     rmarkdown,

diff --git a/R/importDIANN.R b/R/importDIANN.R
@@ -72,7 +72,7 @@ importDIANN <- function(inFile, fileType = "pg_matrix", outLevel = "pg",
                            stopIfEmpty = stopIfEmpty)
 
         sce <- QFeatures::readSummarizedExperiment(
-            inFile, ecol = iCols, sep = "\t", check.names = FALSE, ...
+            inFile, quantCols = iCols, sep = "\t", check.names = FALSE, ...
         )
 
         SummarizedExperiment::assayNames(sce) <- aName

diff --git a/R/importExperiment.R b/R/importExperiment.R
@@ -294,7 +294,7 @@ importExperiment <- function(inFile, iColPattern, includeOnlySamples = "",
 
         if (length(icols) > 0) {
             se <- QFeatures::readSummarizedExperiment(
-                inFile, ecol = icols, sep = "\t", ...
+                inFile, quantCols = icols, sep = "\t", ...
             )
             ## Add list of columns to metadata
             S4Vectors::metadata(se)$cols <- icols