Initial commit

R/primer_table.R

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+#Commentaires lus par roxygen
+#'@include ROBIBarcodes.R
+#'@import XML
+#'
+NULL
+
+#NULL termine le commentaire pour roxygen
+
+extractPrimers <-function(primer){
+  
+  id=xmlAttrs(primer)["ID"]
+  name=xmlValue(xmlChildren(xmlChildren(primer)$name)$text)
+  sequence=xmlValue(xmlChildren(xmlChildren(primer)$sequence)$text)
+  coding=as.logical(xmlValue(xmlChildren(xmlChildren(primer)$coding)$text))
+  
+  p=list(id=id, name=name, sequence=sequence, coding=coding)
+  
+  return(p)
+}
+
+#Export pour rendre publique la fonction
+
+#' Builds primer data frame from metabarcodedb
+#' 
+#' The \code{primers.data.frame} function extracts all the primer information
+#' from the \code{metabarcodedb} database.
+#' 
+#' @param barcodedb a xml document containing a metabarcodedb.
+#' 
+#' @return a \code{data.frame} describing primers.
+#' 
+#' @examples
+#' # load the XML library
+#' library(XML)
+#' 
+#' # load the example metabarcodedb database
+#' db = xmlParseDoc(system.file("extdata/barcodedb.xml", package="ROBIBarcodes"))
+#' 
+#' # extracts the primer table
+#' primers.data.frame(db)
+#' 
+#' @author Aurelie Bonin
+#' @keywords metabarcodes
+#' 
+#' @export
+primers.data.frame <-function(barcodedb){
+  p=getNodeSet(db, 
+               path="/obi:obimetabarcodedb/obi:primers/obi:primer" , 
+               namespaces=c(obi="http://metabarcoding.org/OBIMetabarcodes"))
+
+  primerTable=as.data.frame(do.call(rbind,lapply(p,extractPrimers)))
+
+  rownames(primerTable)=primerTable$id
+  primerTable=primerTable[,-1]
+  
+  return(primerTable)
+}