Merge pull request #8 from nilsmechtel/clean_up

Clean up

.Rbuildignore

@@ -14,10 +14,8 @@
 ^R/do_anova_2w\.R$
 ^R/filter_groupwise\.R$
 ^R/perform_ANOVA\.R$
-
-^R/draw_FC_network\.R$
+^R/two_way_anova\.R$
 ^R/plot_2w_anvova\.R$
-^R/plot_network\.R$
 
 ^tests$
 

DESCRIPTION

@@ -14,23 +14,24 @@ Authors@R:
      person("Daniel", "Huebschmann",
             email = "[email protected]",
             role = c("aut"),
-            comment = c(ORCID = "0000-0002-6041-7049")))
+            comment = c(ORCID = "0000-0002-6041-7049")),
+     person("Luis", "Herfurth",
+            email = "[email protected]",
+            role = c("aut"),
+            comment = c(ORCID = "0009-0000-9933-3056")))
 Depends:
     R (>= 4.0.0)
 Imports:
     openxlsx,
     dplyr,
     tidyr,
-    tibble,
     stringr,
-    ggplot2,
-    ggrepel,
-    methods,
     utils,
     rlang,
-    grDevices,
     SummarizedExperiment,
-    S4Vectors
+    S4Vectors,
+    BiocManager,
+    qvalue
 Description: The 'MetAlyzer' S4 object provides methods to read and reformat metabolomics data for convenient data handling, statistics and downstream analysis. The resulting format corresponds to input data of the Shiny app 'MetaboExtract' (<https://www.metaboextract.shiny.dkfz.de/MetaboExtract/>).
 License: GPL-3
 Encoding: UTF-8

R/plot_log2FC.R

@@ -18,9 +18,11 @@
 #' @export
 #'
 #' @examples
-#' \dontrun{
-#' print(1)
-#' }
+#' metalyzer_se <- MetAlyzer_dataset(file_path = extraction_data())
+#' metalyzer_se <- renameMetaData(metalyzer_se, Method = 'Sample Description')
+#' 
+#' log2FC_df <- calculate_log2FC(metalyzer_se, Method, perc_of_min = 0.2, impute_NA = TRUE)
+#' network <- plot_network(log2FC_df, q_value = 0.05)
 
 # classes <- c('Acylcarnitines', 'Alkaloids', 'Amine Oxides', 'Aminoacids',
 #              'Aminoacids Related', 'Bile Acids', 'Biogenic Amines', 'Carboxylic Acids',