Update BSseq-mod-class.R

R/BSseq-mod-class.R

@@ -9,6 +9,46 @@
     contains = "RangedSummarizedExperiment"
 )
 
+# Validity methods -------------------------------------------------------------
+
+setValidity("BSseq_mod", function(object) {
+    msg <- NULL
+
+    if (identical(object, .BSseq_mod())) {
+        # No validity checks for object returned by internal constructor
+        return(msg)
+    }
+
+    msg <- validMsg(msg, bsseq:::.checkAssayNames(object, c("U", "M", "Other_mod")))
+
+    if(class(rowRanges(object)) != "GRanges") {
+        msg <- validMsg(msg, sprintf("object of class '%s' needs to have a
+                        'GRanges' in slot 'rowRanges'", class(object)))
+    }
+
+    ## benchmarking shows that min(assay()) < 0 is faster than any(assay() < 0) if it is false
+    if(min(assay(object, "M")) < 0 || any(is.null(assay(object, "M"))) ||
+       any(is.infinite(assay(object, "M")))){
+        msg <- validMsg(msg, "the 'M' assay has negative, NA or infinite entries")
+    }
+
+    if(min(assay(object, "U")) < 0 || any(is.null(assay(object, "U"))) ||
+       any(is.infinite(assay(object, "U")))) {
+        msg <- validMsg(msg, "the 'U' assay has negative, NA or infinite entries")
+    }
+
+    if(min(assay(object, "Other_mod")) < 0 || any(is.null(assay(object, "Other_mod"))) ||
+        any(is.infinite(assay(object, "Other_mod")))){
+        msg <- validMsg(msg, "the 'Other_mod' assay has negative, NA or inifinite entries")
+    }
+
+    if (is.null(msg)) {
+        TRUE
+    } else {
+        msg
+    }
+})
+
 # Exported functions -----------------------------------------------------------
 
 # BSseq class object for handling other modification calls generated by modkit