diff read_util.R @ 0:ba070efb6f78 draft

planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/read_util.R	Tue Jul 03 17:34:13 2018 -0400
@@ -0,0 +1,38 @@
+# auxiliar script to help with the read of all R scripts
+read_function <- function(options) {
+
+    # reads the table from input
+    table <- read.delim(options$inputfile_name, header=TRUE, fill=TRUE);
+
+    # get the defined regex from the requested type
+    if (options$type == "lfqlog2") {
+      regexpr <- "LFQ[.]intensity[.]([^[:digit:]]+)[[:digit:]]+";
+      code <- "LFQ";
+    } else if (options$type == "intensity") {
+      regexpr <- "Intensity[.]([^[:digit:]]+)[[:digit:]]+";
+      code <- "INT";
+    } else {
+      regexpr <- "MS[.]MS[.]Count[.]([^[:digit:]]+)[[:digit:]]+";
+      code <- "MS";
+    }
+    if (!(TRUE %in% grepl(regexpr, colnames(table)))) {
+      print (sprintf("Error: No columns of type %s in input table", code));
+      q(1,save="no");
+    }
+
+    # define the columns that will be taken in account for the t-test
+    columns_names <- grep(regexpr, colnames(table), value=TRUE);
+
+    # here I extract the different experiment names in an array for easier
+    # manipulation, ordering them
+    experiment_names <- mixedsort(gsub(".*[.]([^[:digit:]]+[[:digit:]]+).*", "\\1",
+                                        columns_names));
+
+    # extract from the experiment names all the different categories in the table
+    different_categories <- unique(gsub("([^[:digit:]]+).*", "\\1",
+                                        experiment_names));
+
+    read_list <- list(table=table, regex=regexpr, code=code, col_names=columns_names, ex_names=experiment_names, diff_cat=different_categories);
+
+    return(read_list);
+}