make it possible to adjust lts_quantile in Qc-QC-Workflow function

mpc-bioinformatics · Aug 12, 2024 · 5ff79e2 · 5ff79e2
1 parent 1c33dac
commit 5ff79e2
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/R/prepareData.R b/R/prepareData.R
@@ -9,6 +9,7 @@
 #' @param use_groups            If \code{TRUE}, the data contains groups.
 #' @param group_colours         A character vector of hex codes for the group colors, if the data has groups. If \code{NULL}, a default color scale will be used.
 #' @param normalization         A character containing the method of normalization. The possible methods are no normalization "nonorm" or "median", "loess", "quantile" or "lts" normalization.
+#' @param lts_quantile          A numeric containing the quantile for the lts normalization if \code{normalization = "lts"}, default is 0.8.
 #'
 #' @return A list containing the prepared data and the ids of the data as data.frames as well as the groups, number of groups and group colors
 #' @export
@@ -28,7 +29,7 @@ prepareData <- function (data_path,
                          zero_to_NA = TRUE,
                          do_log_transformation = TRUE, log_base = 2,
                          use_groups = FALSE, group_colours = NULL,
-                         normalization = "loess"){
+                         normalization = "loess", lts_quantile = 0.8){
 
 
   #### read and prepare data file ####
@@ -67,7 +68,7 @@ prepareData <- function (data_path,
 
   #### normalize the data ####
 
-  D <- automatedNormalization(DATA = D, method = normalization, is_log_transformed = do_log_transformation, log_base = log_base)
+  D <- automatedNormalization(DATA = D, method = normalization, is_log_transformed = do_log_transformation, log_base = log_base, lts.quantile = lts_quantile)
 
   mess <- paste0(mess, D$message)
   D <- D$data

diff --git a/R/workflow_QC.R b/R/workflow_QC.R
@@ -7,6 +7,7 @@
 # mandatory parameters
 #' @param intensity_columns An integer vector containing the intensity columns of the table.
 #' @param normalization_method A character containing the method of normalization. The possible methods are no normalization "nonorm" or "median", "loess", "quantile" or "lts" normalization.
+#' @param lts_quantile          A numeric containing the quantile for the lts normalization if \code{normalization = "lts"}, default is 0.8.
 #' @param use_groups    If \code{TRUE}, group information encoded in the column names are used. Default is \code{TRUE}.
 #'
 # additional parameters
@@ -80,6 +81,7 @@ workflow_QC <- function(data_path,
 
                         intensity_columns,
                         normalization_method = "loess",
+                        lts_quantile = 0.8,
                         use_groups = TRUE,
 
                         na_strings = c("NA", "NaN", "Filtered","#NV"),
@@ -128,7 +130,7 @@ workflow_QC <- function(data_path,
                                na_strings = na_strings, zero_to_NA = zero_to_NA,
                                do_log_transformation = do_log_transformation, log_base = log_base,
                                use_groups = use_groups, group_colours = group_colours,
-                               normalization = normalization_method)
+                               normalization = normalization_method, lts_quantile = lts_quantile)
 
 
   mess <- paste0(mess, prepared_data[["message"]])#