From e47b2d2e49cd0fe7b4c0ef7597d534574db9475b Mon Sep 17 00:00:00 2001
From: StijnVandenbulcke <vandenbulcke.stijn@gmail.com>
Date: Tue, 7 May 2024 16:52:08 +0200
Subject: [PATCH 1/2] Fixed incorrect subsetting related to the coldata

---
 R/msqrob-methods.R | 42 +++++++++++++++++++++---------------------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/R/msqrob-methods.R b/R/msqrob-methods.R
index 77a6758..f8c9101 100644
--- a/R/msqrob-methods.R
+++ b/R/msqrob-methods.R
@@ -103,32 +103,32 @@ setMethod(
                 "\' in the rowData of the SummarizedExperiment object, set the argument overwrite=TRUE to replace the column with the new results or use another name for the argument modelColumnName to store the results as a novel column in the rowData of SummarizedExperiment object"
             )
         }
-      
+
       if (length(formula) == 3) {
         formula <- formula[-2]
       }
-      
+
       if (any(all.vars(formula) %in% colnames(rowData(object)))){
         stop(
           "Use the msqrobAggregate function to use rowData variables"
         )
       }
-      
-      
-      
-      #Get the variables from the formula and check if they are in the coldata or rowdata 
+
+
+
+      #Get the variables from the formula and check if they are in the coldata or rowdata
       check_vars <- all.vars(formula) %in% colnames(colData(object))
       if (!all(check_vars)){
         if(sum(!check_vars) >1) {
           vars_not_found <- paste0(all.vars(formula)[!check_vars], collapse=", ")
-          stop(paste("Variables", vars_not_found, "are not found in coldata"), sep = "")  
+          stop(paste("Variables", vars_not_found, "are not found in coldata"), sep = "")
         } else{
           vars_not_found <- all.vars(formula)[!check_vars]
-          stop(paste0("Variable ", vars_not_found, " is not found in coldata"), sep = "")  
+          stop(paste0("Variable ", vars_not_found, " is not found in coldata"), sep = "")
         }
       }
-      
-      
+
+
       if (!ridge & is.null(findbars(formula))) {
             rowData(object)[[modelColumnName]] <- msqrobLm(
                 y = assay(object),
@@ -151,7 +151,7 @@ setMethod(
                 lmerArgs = lmerArgs
             )
         }
-      
+
         rowData(object)[[modelColumnName]] <- rowData(object)[[modelColumnName]][rownames(rowData(object))]
         return(object)
     }
@@ -186,34 +186,34 @@ setMethod(
                 "of the QFeatures object, set the argument overwrite=TRUE to replace the column with the new results or use another name for the argument modelColumnName to store the results as a novel column in the rowData of assay of the QFeatures object"
             )
         }
-      
+
       if (length(formula) == 3) {
         formula <- formula[-2]
       }
-      
+
       if (any(all.vars(formula) %in% colnames(rowData(object[[i]])))){
         stop(
           "Use the msqrobAggregate function to use rowData variables"
         )
       }
-      
-      #Get the variables from the formula and check if they are in the coldata or rowdata 
+
+      #Get the variables from the formula and check if they are in the coldata or rowdata
       check_vars <- all.vars(formula) %in% colnames(colData(object))
       if (!all(check_vars)){
         if(sum(!check_vars) >1) {
           vars_not_found <- paste0(all.vars(formula)[!check_vars], collapse=", ")
-          stop(paste("Variables", vars_not_found, "are not found in coldata"), sep = "")  
+          stop(paste("Variables", vars_not_found, "are not found in coldata"), sep = "")
         } else{
           vars_not_found <- all.vars(formula)[!check_vars]
-          stop(paste0("Variable ", vars_not_found, " is not found in coldata"), sep = "")  
+          stop(paste0("Variable ", vars_not_found, " is not found in coldata"), sep = "")
         }
       }
-      
+
       if (!ridge & is.null(findbars(formula))) {
             rowData(object[[i]])[[modelColumnName]] <- msqrobLm(
                 y = assay(object[[i]]),
                 formula = formula,
-                data = droplevels(colData(object)),
+                data = droplevels(colData(getWithColData(object, i = i)))
                 robust = robust,
                 maxitRob = maxitRob
             )
@@ -221,7 +221,7 @@ setMethod(
             rowData(object[[i]])[[modelColumnName]] <- msqrobLmer(
                 y = assay(object[[i]]),
                 formula = formula,
-                data = droplevels(colData(object)),
+                data = droplevels(colData(getWithColData(object, i = i))),
                 rowdata = NULL,
                 robust = robust,
                 ridge = ridge,
@@ -231,7 +231,7 @@ setMethod(
                 lmerArgs = lmerArgs
             )
         }
-      
+
         rowData(object[[i]])[[modelColumnName]] <- rowData(object[[i]])[[modelColumnName]][rownames(rowData(object[[i]]))]
         return(object)
     }

From ae55b186a5878e60a871ae55895c44ebe03bd2ac Mon Sep 17 00:00:00 2001
From: StijnVandenbulcke <vandenbulcke.stijn@gmail.com>
Date: Tue, 7 May 2024 16:54:41 +0200
Subject: [PATCH 2/2] Forgot a comma

---
 R/msqrob-methods.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/msqrob-methods.R b/R/msqrob-methods.R
index f8c9101..b422001 100644
--- a/R/msqrob-methods.R
+++ b/R/msqrob-methods.R
@@ -213,7 +213,7 @@ setMethod(
             rowData(object[[i]])[[modelColumnName]] <- msqrobLm(
                 y = assay(object[[i]]),
                 formula = formula,
-                data = droplevels(colData(getWithColData(object, i = i)))
+                data = droplevels(colData(getWithColData(object, i = i))),
                 robust = robust,
                 maxitRob = maxitRob
             )