fix the shadow matrix

uconn-scs · Jul 25, 2024 · c0ee0ad · c0ee0ad
1 parent 5408a55
commit c0ee0ad
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Showing 2 changed files with 21 additions and 11 deletions.
diff --git a/R/imputations.R b/R/imputations.R
@@ -196,7 +196,8 @@ impute.min_global <- function(dataSet, reportImputing = FALSE) {
   if (reportImputing) {
     ## return the imputed data and the shadow matrix
     return(list(imputedData = imputedData,
-                shadowMatrix = ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0)))
+                shadowMatrix = cbind(dataSet[,c("R.Condition", "R.Replicate")],
+                                     ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0))))
   } else {
     return(imputedData)
   }
@@ -291,7 +292,8 @@ impute.min_local <- function(dataSet, reportImputing = FALSE,
   if (reportImputing) {
     ## return the imputed data and the shadow matrix
     return(list(imputedData = imputedData,
-                shadowMatrix = ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0)))
+                shadowMatrix = cbind(dataSet[,c("R.Condition", "R.Replicate")],
+                                     ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0))))
   } else {
     return(imputedData)
   }
@@ -364,7 +366,8 @@ impute.knn <- function(dataSet, reportImputing = FALSE,
   if (reportImputing) {
     ## return the imputed data and the shadow matrix
     return(list(imputedData = imputedData,
-                shadowMatrix = ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0)))
+                shadowMatrix = cbind(dataSet[,c("R.Condition", "R.Replicate")],
+                                     ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0))))
   } else {
     return(imputedData)
   }
@@ -420,7 +423,8 @@ impute.knn_seq <- function(dataSet, reportImputing = FALSE,
   if (reportImputing) {
     ## return the imputed data and the shadow matrix
     return(list(imputedData = imputedData,
-                shadowMatrix = ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0)))
+                shadowMatrix = cbind(dataSet[,c("R.Condition", "R.Replicate")],
+                                     ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0))))
   } else {
     return(imputedData)
   }
@@ -476,7 +480,8 @@ impute.knn_trunc <- function(dataSet, reportImputing = FALSE,
   if (reportImputing) {
     ## return the imputed data and the shadow matrix
     return(list(imputedData = imputedData,
-                shadowMatrix = ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0)))
+                shadowMatrix = cbind(dataSet[,c("R.Condition", "R.Replicate")],
+                                     ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0))))
   } else {
     return(imputedData)
   }
@@ -565,7 +570,8 @@ impute.nuc_norm <- function(dataSet, reportImputing = FALSE,
   if (reportImputing) {
     ## return the imputed data and the shadow matrix
     return(list(imputedData = imputedData,
-                shadowMatrix = ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0)))
+                shadowMatrix = cbind(dataSet[,c("R.Condition", "R.Replicate")],
+                                     ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0))))
   } else {
     return(imputedData)
   }
@@ -624,7 +630,8 @@ impute.mice_norm <- function(dataSet, reportImputing = FALSE,
   if (reportImputing) {
     ## return the imputed data and the shadow matrix
     return(list(imputedData = imputedData,
-                shadowMatrix = ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0)))
+                shadowMatrix = cbind(dataSet[,c("R.Condition", "R.Replicate")],
+                                     ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0))))
   } else {
     return(imputedData)
   }
@@ -683,7 +690,8 @@ impute.mice_cart <- function(dataSet, reportImputing = FALSE,
   if (reportImputing) {
     ## return the imputed data and the shadow matrix
     return(list(imputedData = imputedData,
-                shadowMatrix = ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0)))
+                shadowMatrix = cbind(dataSet[,c("R.Condition", "R.Replicate")],
+                                     ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0))))
   } else {
     return(imputedData)
   }
@@ -745,7 +753,8 @@ impute.pca_bayes <- function(dataSet, reportImputing = FALSE,
   if (reportImputing) {
     ## return the imputed data and the shadow matrix
     return(list(imputedData = imputedData,
-                shadowMatrix = ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0)))
+                shadowMatrix = cbind(dataSet[,c("R.Condition", "R.Replicate")],
+                                     ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0))))
   } else {
     return(imputedData)
   }
@@ -810,7 +819,8 @@ impute.pca_prob <- function(dataSet, reportImputing = FALSE,
   if (reportImputing) {
     ## return the imputed data and the shadow matrix
     return(list(imputedData = imputedData,
-                shadowMatrix = ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0)))
+                shadowMatrix = cbind(dataSet[,c("R.Condition", "R.Replicate")],
+                                     ifelse(is.na(shadowMatrix) & !is.na(dataPoints), 1, 0))))
   } else {
     return(imputedData)
   }

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   scaffold: scaffold.html
   usage_template: usage_template.html
-last_built: 2024-07-25T04:54Z
+last_built: 2024-07-25T19:05Z
 urls:
   reference: https://uconn-scs.github.io/msDiaLogue/reference
   article: https://uconn-scs.github.io/msDiaLogue/articles