Merge pull request #23 from weaversd/DIANNimport

bug fixes with DIANN import sample count

Author: weaversd

Documentation/Release Updates.txt

@@ -65,4 +65,8 @@ Version 0.1.13
 
 Version 0.1.14
 2024-02-22
-  - Bug fixed for importing peaks files
+  - Bug fixed for importing peaks files
+  
+Version 0.1.15
+2024-07-30
+  - Bug fixed for importing DIANN files where the sample count was calculated improperly when filtering based on Regex.

ui.R

@@ -2,7 +2,7 @@ library(shiny)
 ui <- navbarPage(title = "PrIntMap-R",
                  tabPanel("Documentation",
                           includeMarkdown("Documentation/Documentation.md"),
-                          "Version 0.1.14"), #update version here for each push
+                          "Version 0.1.15"), #update version here for each push
                  tabPanel("Run",
                           flowLayout(
                             fileInput(inputId = "database_file", label = "Upload fasta database file",

www/basic_functions.R

@@ -531,7 +531,7 @@ read_peptide_tsv_DIANN_comb <- function(peptide_file, sample_pattern, sample = N
       names(peptides)[grepl("Stripped.Sequence", names(peptides))] <- "sequence"
       names(peptides)[grepl("Precursor.Quantity", names(peptides))] <- "Intensity"
 
-      sample_count <- length(unique(peptide_import$File.Name))
+      sample_count <- length(unique(peptides$File.Name))
       if (comb_method=="Average"){
         peptides$Intensity <- peptides$Intensity / sample_count
       }
@@ -549,6 +549,7 @@ read_peptide_tsv_DIANN_comb <- function(peptide_file, sample_pattern, sample = N
     }
   } else{
     if (sample_pattern != ""){
+      peptides <- peptide_import
       if(length(names(peptides)[grepl(sample_pattern, names(peptides))])<=0){
         stop("Sample Pattern not found in file.")
       } else {