Change the package path

R/obiclean.R

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+#' @include 02_class_metabarcoding.data.R
+NULL
+
+# TODO: Add comment
+# 
+# Author: coissac
+###############################################################################
+
+#' @export
+setGeneric("extracts.obiclean", function(obj) {
+			return(standardGeneric("extracts.obiclean"))
+		})
+
+#' Extracts the obiclean results
+#' 
+#' The method \code{extracts.obiclean} of the class \code{\linkS4class{metabarcoding.data}}
+#' extracts \code{obiclean} results from the MOTUs descriptions include in the 
+#' \code{\linkS4class{metabarcoding.data}} instance. 
+#' When an \code{obitab} file is imported using the \code{\link{import.metabarcoding.data}}
+#' if \code{obiclean} results are present in the file they are stored in the 
+#' \code{motu} data.frame. By calling this methods, MOTU descriptors describing 
+#' the \code{obiclean} status are moved to a set of layers.
+#' 
+#' @param obj the \code{\linkS4class{metabarcoding.data}} to analyze
+#' 
+#' @return the modified \code{\linkS4class{metabarcoding.data}} instance
+#' 
+#' @examples
+#' 
+#' # load termite data set from the ROBITools sample data
+#' data(termes)
+#' 
+#' # shows the initial list of layer names
+#' layer.names(t)
+#' 
+#' # extracts the obiclean status
+#' termes = extracts.obiclean(termes)
+#' 
+#' # shows the name of the newly created layers
+#' layer.names(t)
+#' 
+#' 
+#' 
+#' @seealso \code{\linkS4class{metabarcoding.data}}, \code{\link{threshold.mask}}, \code{\link{normalize}}
+#'
+#' @docType methods
+#' @rdname extracts-obiclean-methods
+#' @aliases extracts.obiclean-methods,metabarcoding.data
+#' @author Eric Coissac
+#' 
+
+
+setMethod("extracts.obiclean", "metabarcoding.data", function(obj) {
+  
+			pat = "^obiclean_status:.*$"
+			cols = colnames(obj@motus)
+			cleancols = grep(pat,cols)
+			clean.names=cols[cleancols]
+      p = grep(pat,cols)
+      d = t(as.factor.or.matrix(obj@motus[,p]))
+      n = sapply(strsplit(cols[p],':'),function(y) y[[2]])
+      rownames(d)=n
+      d = d[rownames(obj@reads),]
+      obj[["obiclean_status"]]=d
+      
+      newmotus = obj@motus[-cleancols]
+      
+			pat = "^obiclean_count:.*$"
+			cols = colnames(newmotus)
+			cleancols = grep(pat,cols)
+			clean.names=cols[cleancols]
+			p = grep(pat,cols)
+			d = t(as.factor.or.matrix(newmotus[,p]))
+			n = sapply(strsplit(cols[p],':'),function(y) y[[2]])
+			rownames(d)=n
+			d = d[rownames(obj@reads),]
+			obj[["obiclean_count"]]=d
+			
+			newmotus = newmotus[-cleancols]
+			
+			pat = "^obiclean_cluster:.*$"
+			cols = colnames(newmotus)
+			cleancols = grep(pat,cols)
+			clean.names=cols[cleancols]
+			p = grep(pat,cols)
+			d = t(as.factor.or.matrix(newmotus[,p]))
+			n = sapply(strsplit(cols[p],':'),function(y) y[[2]])
+			rownames(d)=n
+			d = d[rownames(obj@reads),]
+			obj[["obiclean_cluster"]]=d
+			
+			newmotus = newmotus[-cleancols]
+			
+			newdata = copy.metabarcoding.data(obj,motus=newmotus)
+      
+			return(newdata)
+		})
+
+
+#' @export
+setGeneric("extracts.obiclean_cluster", function(obj) {
+  return(standardGeneric("extracts.obiclean_cluster"))
+})
+
+setMethod("extracts.obiclean_cluster", "metabarcoding.data", function(obj) {
+ 
+    obiclean = extracts.obiclean(obj)
+    obihead  = obiclean[,! is.na(obiclean$motus$obiclean_head)]
+    obihead$obiclean_count[is.na(obihead$obiclean_count)]=0
+    reads = obihead$obiclean_count
+    
+    l = obihead@layers[layer.names(obihead) != "obiclean_count"]
+    
+    newdata = copy.metabarcoding.data(obihead,reads=reads,layers=l)
+    
+    return(newdata)
+}
+)