Change the package path

R/export-metabarcoding.R

@@ -0,0 +1,62 @@
+#' @include 02_class_metabarcoding.data.R
+NULL
+
+
+# TODO: Add comment
+# 
+# Author: coissac
+###############################################################################
+
+require(utils)
+
+expand.metabarcoding.data=function(data,minread=1) {
+	resultonesample=function(sample) {
+		mo= data@reads[sample,] >= minread
+		s = data@samples[rep(sample,sum(mo)),]
+		r = as.numeric(data@reads[sample,mo])
+		m = data@motus[mo,]
+		
+		result = data.frame(s,frequency=r,m, 
+				stringsAsFactors =FALSE,
+				row.names = NULL)
+		
+		result
+	}
+	
+	res = lapply(1:data@scount, resultonesample)
+	
+	do.call(rbind,res)	
+}
+
+#setGeneric("utils::write.csv")
+write.csv.metabarcoding.data = function(...) {
+	Call <- match.call(expand.dots = TRUE)
+	if (!is.null(Call[["minread"]])) {
+		minread = Call[["minread"]]
+		Call = Call[!names(Call)=="minread"]
+	}
+	else
+		minread = 1
+	data = eval.parent(Call[[2L]])
+	data = expand.metabarcoding.data(data,minread)
+	Call[[1L]] <- as.name("write.csv")
+	Call[[2L]] <- as.name("data")
+	eval(Call)
+}
+
+#setGeneric("utils::write.csv2")
+write.csv2.metabarcoding.data = function(...) {
+	Call <- match.call(expand.dots = TRUE)
+	if (!is.null(Call[["minread"]])) {
+		minread = Call[["minread"]]
+		Call = Call[!names(Call)=="minread"]
+	}
+	else
+		minread = 1
+	data = eval.parent(Call[[2L]])
+	data = expand.metabarcoding.data(data,minread)
+	Call[[1L]] <- as.name("write.csv2")
+	Call[[2L]] <- as.name("data")
+	eval(Call)
+	
+}