change argument to to_wide accept all value vars

Author: wolski

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: prolfqua
 Type: Package
 Title: Proteomics Label Free Quantification
-Version: 1.3.8
+Version: 1.3.9
 Authors@R: c(person("Witold", "Wolski",
         email = "wew@fgcz.ethz.ch",
         role = c("aut", "cre"),
@@ -70,7 +70,7 @@ Suggests:
     SummarizedExperiment,
     proDA,
     vsn
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Roxygen: list(r6 = TRUE)
 Depends: 
     R (>= 4.1)

NAMESPACE

@@ -56,6 +56,7 @@ export(filter_byQValue)
 export(filter_difference)
 export(filter_proteins_by_peptide_count)
 export(find_package_file)
+export(function_lod_quantile)
 export(generate_contrasts)
 export(generate_contrasts_for_factor)
 export(get_UniprotID_from_fasta_header)
@@ -67,6 +68,7 @@ export(get_robscales)
 export(group_label)
 export(hierarchy_counts)
 export(hierarchy_counts_sample)
+export(impute_with_zcomp)
 export(intensity_summary_by_hkeys)
 export(interaction_contrasts)
 export(interaction_missing_stats)

R/LFQData.R

@@ -164,17 +164,18 @@ LFQData <- R6::R6Class(
     #' @description
     #' converts the data to wide
     #' @param as.matrix return as data.frame or matrix
-    #' @param value either response or nr chidren
+    #' @param value see possible lfqdata$config$table$value_vars()
     #' @return list with data, annotation, and configuration
-    to_wide = function(as.matrix = FALSE, value = c("response", "nr_children")){
-      value <- match.arg(value)
-      if (value == "response") {
+    #'
+    to_wide = function(as.matrix = FALSE, value = NULL){
+      if (is.null(value)) {
         wide <- prolfqua::tidy_to_wide_config(self$data, self$config, as.matrix = as.matrix)
       } else {
+        stopifnot(value %in% self$config$table$value_vars())
         wide <- prolfqua::tidy_to_wide_config(
           self$data, self$config,
           as.matrix = as.matrix,
-          value = self$config$table$nr_children)
+          value = value)
       }
       wide$config <- self$config$clone(deep = TRUE)
       return(wide)

R/LFQDataImp.R

@@ -18,13 +18,14 @@ estimate_lod_global <- function(data_matrix, prop_na = 90) {
 
 
 #' get smallest values per sample
+#' @export
 #' @examples
 #' # example code
 #'
 #' istar <- sim_lfq_data_peptide_config()
 #' lfqdata <- LFQData$new(istar$data, istar$config)
 #' xx <- lfqdata$to_wide(as.matrix=TRUE)
-#' s <- function_log_quantile(xx$data)
+#' s <- function_lod_quantile(xx$data)
 #' sapply(s, median)
 #' sapply(s, mean)
 function_lod_quantile <- function(data_matrix, percent = 10) {