Differences

This shows you the differences between two versions of the page.

--- half_matrix [2008/01/29 10:31] – heidi
+++ half_matrix [2008/09/23 09:44] (current) – heidi
@@ Line 48: / Line 48: @@
 numericMatrix
 </code>
+===== read half matrix out of full matrix =====
+  * file: read_tag-halfOutOfFullMatrix.r
+\\
+**code:**
+<code>
+#----open XML package-----------------------------------------------------------
+library(XML)
+#----read data between an XML tag-----------------------------------------------
+filename = "D:/Master/R_Daten/XML/PairwiseFst_XML2.xml"   #not correct!!!!
+tag = "//Fst"
+doc = xmlTreeParse(filename, useInternal = TRUE)
+ch = getNodeSet(doc, tag)
+subDoc = xmlDoc(ch[[1]])
+tagData <- xpathApply(subDoc, tag, xmlValue)
+free(subDoc)
+ #----convert string data (half out of a full matrix) to a numeric matrix------
+  #----split string----
+  tagData2 <- as.character(xmlText)
+  tagData3 <- strsplit(tagData2, "\n")
+  tagMatrix <- as.matrix(as.data.frame(tagData3))
+  tagMatrix <- gsub(" + ", " ", tagMatrix)   # trim white space
+  tagMatrix <- tagMatrix[4:(nrow(tagMatrix)-1)]
+  Data <- strsplit(tagMatrix, " ")
+  #----to numeric matrix----
+  Row <- length(Data)
+  Matrix <- matrix(NA, ncol=1, nrow=Row)
+  numericList <- as.numeric(Matrix)
+  numericMatrix <- t(as.matrix(numericList))
+  for(n in 2:(Row)){
+    nextrow <- as.matrix(as.data.frame(Data[[n]][3:(n+1)]))
+    nextrow <- rbind(nextrow, matrix(NA, ncol=1, nrow=(Row-(n-1))))
+    #nextrow <- nextrow[3:nrow(nextrow),]
+    numericList <- as.numeric(nextrow)
+    numericMatrix <- rbind(numericMatrix, t(as.matrix(numericList)))
+  }
+  numericMatrix
+</code>