add option to generate sample names from raw.file or factors or provi…

…de in annotation
fgcz · Dec 13, 2023 · 9da83de · 9da83de
1 parent db51cad
commit 9da83de
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Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/R/AnalysisConfiguration.R b/R/AnalysisConfiguration.R
@@ -129,7 +129,7 @@ R6_extract_values <- function(r6class){
 #' sample_analysis <- setup_analysis(prolfqua_data('data_skylinePRMSample_A')$data, skylineconfig)
 #'
 
-setup_analysis <- function(data, configuration, cc = TRUE ){
+setup_analysis <- function(data, configuration, cc = TRUE,  from_factors = FALSE){
   configuration <- configuration$clone(deep = TRUE)
   table <- configuration$table
 
@@ -159,7 +159,7 @@ setup_analysis <- function(data, configuration, cc = TRUE ){
 
   sampleName <- table$sampleName
 
-  if (FALSE & !sampleName  %in% names(data)) {
+  if (from_factors & !sampleName  %in% names(data)) {
     message("creating sampleName from factor columns")
     data <- data |>  tidyr::unite(
       UQ(sym(sampleName)) ,

diff --git a/R/AnalysisTableAnnotation.R b/R/AnalysisTableAnnotation.R
@@ -28,7 +28,7 @@ AnalysisTableAnnotation <- R6::R6Class(
 
     #' @field fileName column name of column containing raw file names
     fileName = NULL,
-    #' @field sampleName (will be generated from factors)
+    #' @field sampleName (will be generated from factors or fileName)
     sampleName = "sampleName",
 
     #' @field isotopeLabel which column contains the isotope label (e.g. heavy or light), Gor light only if LFQ.

diff --git a/man/AnalysisTableAnnotation.Rd b/man/AnalysisTableAnnotation.Rd
diff --git a/man/setup_analysis.Rd b/man/setup_analysis.Rd