fix examples

fgcz · Apr 30, 2024 · 2a8fd62 · 2a8fd62
1 parent 5eaed53
commit 2a8fd62
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Showing 21 changed files with 2 additions and 34 deletions.
diff --git a/R/A_dataset_docu.R b/R/A_dataset_docu.R
@@ -76,16 +76,6 @@ NULL
 "data_SAINTe_output"
 
 
-#' Model for debugging
-#' @family data
-#' @keywords internal
-#' @docType data
-#' @format a linear model
-"data_modellingResult_A"
-
-# #@usage data_modellingResult_A <- prolfqua_data("data_modellingResult_A")
-
-
 
 #' Model for debugging
 #' @family data

diff --git a/R/tidyMS_R6_Modelling.R b/R/tidyMS_R6_Modelling.R
@@ -567,9 +567,9 @@ linfct_from_model <- function(m, as_list = TRUE){
 build_models <- function(model = c("factors", "interaction"), Nprot = 10, with_missing = TRUE, weight_missing = 1) {
   model <- match.arg(model)
   model <- if (model == "factors") {
-     "~ Treatment * Background"
+     "~ Treatment + Background"
   } else {
-    "~ Treatment + Background"
+    "~ Treatment * Background"
   }
   istar <- prolfqua::sim_lfq_data_protein_2Factor_config(Nprot = Nprot, with_missing = with_missing, weight_missing = weight_missing)
   istar <- prolfqua::LFQData$new(istar$data,istar$config)
@@ -984,8 +984,6 @@ pivot_model_contrasts_2_Wide <- function(modelWithInteractionsContrasts,
 #' @export
 #' @keywords internal
 #' @examples
-#' #data("data_modellingResult_A")
-#' #modelSummary_A <- data_modellingResult_A
 #' modelSummary_A <- build_models()
 #' m <- get_complete_model_fit(modelSummary_A$modelDF)
 #'

diff --git a/man/PACKAGE_DATA.Rd b/man/PACKAGE_DATA.Rd
diff --git a/man/contrasts_linfct.Rd b/man/contrasts_linfct.Rd
diff --git a/man/data_IonstarProtein_subsetNorm.Rd b/man/data_IonstarProtein_subsetNorm.Rd
diff --git a/man/data_SAINTe_output.Rd b/man/data_SAINTe_output.Rd
diff --git a/man/data_Yeast2Factor.Rd b/man/data_Yeast2Factor.Rd
diff --git a/man/data_basicModel_p1807.Rd b/man/data_basicModel_p1807.Rd
diff --git a/man/data_benchmarkExample.Rd b/man/data_benchmarkExample.Rd
diff --git a/man/data_checksummarizationrobust87.Rd b/man/data_checksummarizationrobust87.Rd
diff --git a/man/data_checksummarizerobust.Rd b/man/data_checksummarizerobust.Rd
diff --git a/man/data_checksummarizerobust69.Rd b/man/data_checksummarizerobust69.Rd
diff --git a/man/data_correlatedPeptideList.Rd b/man/data_correlatedPeptideList.Rd
diff --git a/man/data_interactionModel_p1807.Rd b/man/data_interactionModel_p1807.Rd
diff --git a/man/data_ionstar.Rd b/man/data_ionstar.Rd
diff --git a/man/data_multigroupFC.Rd b/man/data_multigroupFC.Rd
diff --git a/man/data_skylinePRMSample_A.Rd b/man/data_skylinePRMSample_A.Rd
diff --git a/man/data_skylineSRM_HL_A.Rd b/man/data_skylineSRM_HL_A.Rd
diff --git a/man/data_spectronautDIA250_A.Rd b/man/data_spectronautDIA250_A.Rd
diff --git a/man/data_test_confusion_matrix_scores.Rd b/man/data_test_confusion_matrix_scores.Rd
diff --git a/man/prolfqua_data.Rd b/man/prolfqua_data.Rd