adding nr_children to LFQData and LFQDataAggregator

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: prolfqua
 Type: Package
 Title: Proteomics Label Free Quantification
-Version: 1.2.1
+Version: 1.2.2
 Authors@R: c(person("Witold", "Wolski",
         email = c("[email protected]", "[email protected]"),
         role = c("aut", "cre"),

R/ContrastsProDA.R

@@ -4,24 +4,23 @@
 #' @family modelling
 #' @examples
 #'
-#' istar <- prolfqua_data('data_ionstar')$normalized()
-#' istar$config <- old2new(istar$config )
-#' istar_data <- dplyr::filter(istar$data ,protein_Id %in% sample(protein_Id, 10))
+#' istar <- prolfqua::sim_lfq_data_peptide_config()
+#' istar$config <- istar$config
+#' istar_data <- istar$data
 #' lfd <- LFQData$new(istar_data, istar$config)
-#' #debug(prolfqua::LFQDataToSummarizedExperiment)
 #' se <- prolfqua::LFQDataToSummarizedExperiment(lfd)
 #'
-#' fit <- proDA::proDA(se, design = ~ dilution. - 1,data_is_log_transformed = TRUE)
+#' fit <- proDA::proDA(se, design = ~ group_ - 1, data_is_log_transformed = TRUE)
 #' contr <- list()
 #'
-#' contrasts <- c("dilution_(9/7.5)_1.2" = "dilution.e - dilution.d",
-#'                "dilution_(7.5/6)_1.25" = "dilution.d - dilution.c")
-#' contr[["dilution_(9/7.5)_1.2"]] <- data.frame(
-#'   contrast = "dilution_(9/7.5)_1.2",
-#'   proDA::test_diff(fit, contrast = "dilution.e - dilution.d"))
-#' contr[["dilution_(7.5/6)_1.25"]] <- data.frame(
-#'   contrast = "dilution_(7.5/6)_1.25",
-#'   proDA::test_diff(fit, contrast = "dilution.d - dilution.c"))
+#' contrasts <- c("group_AvsCtrl" = "group_A - group_Ctrl",
+#'                "group_BvsCtrl" = "group_B - group_Ctrl")
+#' contr[["group_AvsCtrl"]] <- data.frame(
+#'   contrast = "group_AvsCtrl",
+#'   proDA::test_diff(fit, contrast = "group_A - group_Ctrl"))
+#' contr[["group_BvsCtrl"]] <- data.frame(
+#'   contrast = "group_BvsCtrl",
+#'   proDA::test_diff(fit, contrast = "group_B - group_Ctrl"))
 #'
 #' bb <- dplyr::bind_rows(contr)
 #' cproDA <- ContrastsProDA$new(bb, contrasts = contrasts, subject_Id = "name")

R/LFQData.R

@@ -169,9 +169,18 @@ 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
     #' @return list with data, annotation, and configuration
-    to_wide = function(as.matrix = FALSE){
-      wide <- prolfqua::tidy_to_wide_config(self$data, self$config, as.matrix = as.matrix)
+    to_wide = function(as.matrix = FALSE, value = c("response", "nr_children")){
+      value <- match.arg(value)
+      if (value == "response") {
+        wide <- prolfqua::tidy_to_wide_config(self$data, self$config, as.matrix = as.matrix)
+      } else {
+        wide <- prolfqua::tidy_to_wide_config(
+          self$data, self$config,
+          as.matrix = as.matrix,
+          value = self$config$table$nr_children)
+      }
       wide$config <- self$config$clone(deep = TRUE)
       return(wide)
     },
@@ -275,9 +284,6 @@ LFQData <- R6::R6Class(
 )
 
 
-
-
-
 #' converts LFQData object to SummarizedExperiment
 #'
 #' For compatibility with Bioconductor
@@ -287,9 +293,9 @@ LFQData <- R6::R6Class(
 #' @export
 #' @examples
 #'
-#' istar <- prolfqua_data('data_ionstar')
-#' istar$config <- old2new(istar$config)
-#' data <- istar$data |> dplyr::filter(protein_Id %in% sample(protein_Id, 100))
+#' istar <- prolfqua::sim_lfq_data_peptide_config()
+#' istar$config <- (istar$config)
+#' data <- istar$data
 #' lfqdata <- LFQData$new(data, istar$config)
 #' lfqdata$to_wide()
 #' if(require("SummarizedExperiment")){
@@ -299,10 +305,14 @@ LFQData <- R6::R6Class(
 LFQDataToSummarizedExperiment <- function(lfqdata){
   if (requireNamespace("SummarizedExperiment")) {
     wide <- lfqdata$to_wide(as.matrix = TRUE)
+    nr_children <- lfqdata$to_wide(as.matrix = TRUE, value = "nr_children")
     ann <- data.frame(wide$annotation)
     rownames(ann) <- wide$annotation[[lfqdata$config$table$sampleName]]
-    se <- SummarizedExperiment::SummarizedExperiment(S4Vectors::SimpleList(LFQ = wide$data), colData = ann,
-                                                     rowData = wide$rowdata)
+    se <- SummarizedExperiment::SummarizedExperiment(S4Vectors::SimpleList(
+      LFQ = wide$data,
+      nr_children = nr_children$data),
+      colData = ann,
+      rowData = wide$rowdata)
     return(se)
   }
 }

R/tidyMS_R6_TransitionCorrelations.R

@@ -226,9 +226,9 @@ tidy_to_wide <- function(data,
 #' testthat::expect_equal(nrow(res$rowdata), nrow(res$data))
 #' testthat::expect_equal(ncol(res$data) - ncol(res$rowdata) , nrow(res$annotation))
 #' res <- tidy_to_wide_config(data, config, as.matrix = TRUE)
-#' dim(res$data) == c(28,  12)
-#' dim(res$annotation) == c(12,  3)
-#' dim(res$rowdata) == c(28, 3)
+#' stopifnot(all(dim(res$data) == c(28,  12))
+#' stopifnot(all(dim(res$annotation) == c(12,  4)))
+#' stopifnot(all(dim(res$rowdata) == c(28, 3)))
 #'
 #' res <- scale(res$data)
 #' tidy_to_wide_config(data, config,  value = config$table$nr_children)
@@ -239,6 +239,8 @@ tidy_to_wide <- function(data,
 #' #xt$config$table$is_response_transformed <- TRUE
 #' res <- xt$get_Aggregator()
 #' x <- res$medpolish()
+#' towide <- tidy_to_wide_config(x$data, x$config,  value = x$config$table$nr_children)
+#'
 #' dd <- prolfqua::sim_lfq_data_protein_config()
 #' dd$config$table$nr_children
 #' dd$data