[Qpcr-commits] r94 - pkg/NormqPCR/R

[noreply at r-forge.r-project.org]

Author: jperkins
Date: 2010-02-25 18:51:31 +0100 (Thu, 25 Feb 2010)
New Revision: 94

Added:
   pkg/NormqPCR/R/dealWithNA.R
Log:
allows the user to deal with NAs themselves. Means we can just do mean, na.rm = T and not have to worry

Copied: pkg/NormqPCR/R/dealWithNA.R (from rev 90, pkg/NormqPCR/R/dealWithUndetermined.R)
===================================================================
--- pkg/NormqPCR/R/dealWithNA.R	                        (rev 0)
+++ pkg/NormqPCR/R/dealWithNA.R	2010-02-25 17:51:31 UTC (rev 94)
@@ -0,0 +1,46 @@
+#######################################################
+# replaceNAs - this replaces all NAs with a set number
+setGeneric("replaceNAs",
+  function(qPCRBatch, newNA=40)
+  standardGeneric("replaceNAs")
+)
+setMethod("replaceNAs", signature = "qPCRBatch", definition =
+  function(qPCRBatch, newNA) {
+    exprs(qPCRBatch)[is.na(exprs(qPCRBatch))] <- newNA
+    return(qPCRBatch)
+  }
+)
+###############################################################################################
+# replaceAboveCutOff - this replaces anything above a given number with a (supplied) new value
+setGeneric("replaceAboveCutOff",
+  function(qPCRBatch, newVal=NA, cutOff=38)
+  standardGeneric("replaceAboveCutOff")
+)
+setMethod("replaceAboveCutOff", signature = "qPCRBatch", definition =
+  function(qPCRBatch, newVal, cutOff) {
+    exprs(qPCRBatch)[exprs(qPCRBatch) > cutOff] <- newVal
+    return(qPCRBatch)
+  }
+)
+################################################################################################################
+# makeAllNAs - for each detector, if you have > a given number of NAs, then all values are all replaced with NA
+# This means we can ignore any NAs in future calculations (since they can be dealt with using these functions
+setGeneric("makeAllNAs",
+  function(qPCRBatch, maxNACase, maxNAControl, contrastM, case, control)
+  standardGeneric("makeAllNAs")
+)
+setMethod("makeAllNAs", signature = "qPCRBatch", definition =
+  function(qPCRBatch, maxNACase, maxNAControl, contrastM, case, control) {
+    case <- row.names(contrastM)[contrastM[,case] == 1]
+    control <- row.names(contrastM)[contrastM[,control] == 1]
+    expM <- exprs(qPCRBatch)
+    caseM <- expM[,case]
+    controlM <- expM[,control]
+
+    for (detector in featureNames(qPCRBatch)) {
+      if(sum(is.na(expM[detector,case])) > maxNACase) caseM[detector,case] <- NA
+      if(sum(is.na(expM[detector,control])) > maxNAControl) controlM[detector,case] <- NA
+    }
+    return(qPCRBatch)
+  }
+)