Change the package path

R/rarefy.R

@@ -0,0 +1,99 @@
+#' @include 02_class_metabarcoding.data.R
+NULL
+
+# TODO: Add comment
+# 
+# Author: coissac
+###############################################################################
+
+#' @export
+setGeneric("rarefy", function(x,n,first.pass=0.95,pseudo.count=0,...) {
+			return(standardGeneric("rarefy"))
+		})
+
+setMethod("rarefy", "ANY", function(x,n,first.pass=0.95,pseudo.count=0,sum=NA) {
+				
+	if (is.na(sum))
+		sum=sum(x)
+
+	if (sum < sum(x))
+		stop("sum parameter must be greater or equal to sum(x)")
+  
+  grey = sum-sum(x)
+	
+	probs = x + pseudo.count
+  
+  if (grey > 0)
+	  probs = c(probs,grey)
+	
+	# Just to ensure at least one execution of the loop
+	n1 = n * 2
+	
+	while(n1 > n)
+		n1 = rpois(1,n * first.pass)
+	
+	rep1 = as.vector(rmultinom(1,n1,probs))
+	n2  = sum(rep1)
+	
+	levels = 1:length(probs)
+	
+	rep2= as.vector(table(factor(sample(levels,
+						   	                      n - n2,
+							                        replace=TRUE, 
+							                        prob = probs),
+					                            levels=levels)))
+	
+	rep1 = (rep1 + rep2)
+  
+  if (grey > 0)
+    rep1 = rep1[-length(rep1)]
+  
+	return(rep1)
+})
+
+
+setMethod("rarefy", "metabarcoding.data", function(x,n,first.pass=0.95,pseudo.count=0,MARGIN='sample') {
+		
+	if (MARGIN == 'sample')
+		MARGIN=1
+	
+	if (MARGIN == 'motu')
+		MARGIN=2
+	
+  dreads= dim(x@reads)
+  rreads= matrix(0,nrow = dreads[1] , ncol = dreads[2])
+	
+	if (MARGIN == 1)
+      for (i in 1:dreads[1]) {
+        rreads[i,]=rarefy(x@reads[i,],
+                          n=n,
+                          first.pass=first.pass,
+                          pseudo.count=pseudo.count)
+      }
+    
+# 		rreads = t(apply(reads,1,rarefy,n=n,
+# 					 	 first.pass=first.pass,
+# 						 pseudo.count=pseudo.count))
+	else
+	  for (i in 1:dreads[2]) {
+	    rreads[,i]=rarefy(x@reads[,i],
+	                      n=n,
+	                      first.pass=first.pass,
+	                      pseudo.count=pseudo.count)
+	  }
+
+# rreads =   as.matrix(apply(reads,2,rarefy,n=n,
+# 								   first.pass=first.pass,
+# 								   pseudo.count=pseudo.count))
+
+  rreads=as.matrix(rreads)
+			
+	rownames(rreads) = rownames(x@reads)
+	colnames(rreads) = colnames(x@reads)
+	
+	newdata = copy.metabarcoding.data(x,reads=rreads)
+	
+	return(newdata)
+	
+})
+