fix bug

tidymass · May 17, 2023 · f09e4ce · f09e4ce
1 parent 8b09e70
commit f09e4ce
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Showing 4 changed files with 28 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: masscleaner
 Type: Package
 Title: Data cleaning for LC-MS based metabolomics data
-Version: 1.0.10
+Version: 1.0.11
 Date: 2023-05-16
 Authors@R: c(person(given = "Xiaotao",
            family = "Shen",

diff --git a/NEWS.md b/NEWS.md
@@ -91,3 +91,7 @@
 # Version 1.0.10 (20230516)
 --------------
 * Fixed bug in normalize_data function.
+
+# Version 1.0.10 (20230517)
+--------------
+* Fixed bug in normalize_data function.
diff --git a/R/check_data.R b/R/check_data.R
@@ -38,6 +38,11 @@ check_for_qc_normalization <-
     sample_info <-
       object@sample_info
 
+    ###remove blank samples
+    sample_info <-
+      sample_info %>% 
+      dplyr::filter(!is.na(injection.order))
+
     purrr::map(
       unique(sample_info$batch),
       .f = function(batch_idx) {

diff --git a/R/normalize_data.R b/R/normalize_data.R
@@ -62,7 +62,7 @@ normalize_data <-
       new_expression_data <-
         normalize_data_total(x = expression_data, keep_scale = keep_scale)
 
-      object@expression_data <- 
+      object@expression_data <-
         as.data.frame(new_expression_data)
 
       parameter <- new(
@@ -78,7 +78,7 @@ normalize_data <-
     if (method == "mean") {
       new_expression_data <-
         normalize_data_mean(x = expression_data, keep_scale = keep_scale)
-      object@expression_data <- 
+      object@expression_data <-
         as.data.frame(new_expression_data)
 
       parameter <- new(
@@ -94,7 +94,7 @@ normalize_data <-
     if (method == "median") {
       new_expression_data <-
         normalize_data_median(x = expression_data, keep_scale = keep_scale)
-      object@expression_data <- 
+      object@expression_data <-
         as.data.frame(new_expression_data)
 
       parameter <- new(
@@ -232,9 +232,24 @@ normalize_data <-
         stop("No Subject in your sample_info column 'class'")
       }
 
+      sample_info <-
+        sample_info %>%
+        dplyr::mutate(batch = as.character(batch))
+
+      sample_info$batch[sample_info$class != "QC" &
+                          sample_info$class != "Subject"] <-
+        NA
+
+      sample_info$batch[is.na(sample_info$batch)] <- "NA"
+
       data_nor <-
         purrr::map(unique(sample_info$batch), function(batch_idx) {
           message(crayon::yellow("Batch", batch_idx, "..."))
+          if (batch_idx == "NA") {
+            new_data <-
+              expression_data[, sample_info$batch == batch_idx]
+            return(new_data)
+          }
           subject_id <-
             sample_info %>%
             dplyr::filter(class == "Subject" &