Major development changes: SIAMCAT object structure, constructor function, pipeline versatility, vignettes, and several smaller bugfixes

Major development changes:

• The SIAMCAT object structure has changed: new slots for filtered and normalised data, also for association results
• The constructor function takes named arguments now and runs validate.data by default
• Pipeline versatility has been increased: by using feature.type, every function working with features can work on either the original, the filtered, or the normalised features
• Updated data input vignette, included holdout testing vignette
• Smaller bugfixes in almost every function in order to make it compatible with the new package structure and pipeline versatility
• read.features and read.meta have been deprecated
• Rscript flavour has been updated for the CI with the new package structure

R/read_label.r

@@ -115,7 +115,7 @@ trim <- function(x) {
 }
 
 #' @title Parse label header
-#'
+#'A
 #' @description This function parses the header of a label file
 #'
 #' @param  label.header - string in the format: #<TYPE>:<L1>=<class1>;