--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mosaics/R/AllClasses.R	Thu Jan 10 16:01:28 2013 -0500
@@ -0,0 +1,81 @@
+
+# obtained from importing bin-level data obtained from perl codes
+
+setClass( Class="BinData",
+    representation=representation(
+        chrID="character",
+        coord="numeric",
+        tagCount="numeric",
+        mappability="numeric",
+        gcContent="numeric",
+        input="numeric",
+        dataType="character"
+    )
+)
+
+# obtained from MOSAiCS Z0 & Z1 model fit
+
+setClass( Class="MosaicsFitEst",
+    representation=representation(
+        pi0="numeric",
+        a="numeric",
+        betaEst="numeric",
+        muEst="numeric",    
+        pNfit="list",
+        b="numeric",
+        c="numeric",
+        p1="numeric",
+        b1="numeric",
+        c1="numeric",
+        b2="numeric",
+        c2="numeric",
+        inputTrunc="numeric",
+        analysisType="character"
+    )
+)
+
+setClass( Class="MosaicsFitParam",
+    representation=representation(
+        k="numeric",
+        meanThres="numeric",
+        s="numeric",
+        d="numeric"
+    )
+)
+
+setClass( Class="MosaicsFit",
+    representation=representation(
+        mosaicsEst="MosaicsFitEst",
+        mosaicsParam="MosaicsFitParam",
+        chrID="character",
+        coord="numeric",
+        tagCount="numeric",
+        mappability="numeric",
+        gcContent="numeric",
+        input="numeric",
+        bic1S="numeric",
+        bic2S="numeric"
+    )
+)
+
+# obtained from final MOSAiCS peak calling
+
+setClass( Class="MosaicsPeakParam",
+    representation=representation(
+        analysisType="character",
+        signalModel="character",
+        FDR="numeric",
+        maxgap="numeric",
+        minsize="numeric",
+        thres="numeric"
+    )
+)
+
+setClass( Class="MosaicsPeak",
+    representation=representation(
+        peakList="data.frame",
+        peakParam="MosaicsPeakParam",
+        bdBin="data.frame",
+        empFDR="numeric"
+    )
+)