Cluster

Public Methods

• Cluster - public constructor
• Copy - used to copy an instance of a cluster
• SetMatric (char,char,char) - set up distance function and hierarchical clustering method
• Hierarchical (DataGrouping) - save all of clustering results (cdt,atr,gtr)

Private Methods

• cValue - struct, used to hold index and its value
• Asc - sort rows/columns by ascending order
• Sort(int, double, ref SortedList)- sets up an index table given the data, such that data[index[]] is in increasing order
• TreeSort (char,int,double[,],int[,],int[,]) - sort data set according to cluster result
• SaveCluster (string,bool,bool,DataGrouping)- save cluster data table
• distancematrix (int) - initialize matrix to be calculated and get uccorrelation results
• Ucorrelation (int,int,int,int) - Calculates the weighted pearson distance between two rows or columns, using the uncenerted version of the pearson correlation
• Correlation (int,int,int,int) - Calculates the Pearson distance between two rows or columns in a matrix.
• Spearman (int,int,int,int) - Calculates the Spearman's rank distance between two rows or columns in a matrix.
• GetRank (int,double,double) - Calculate the ranks of the elements in the array data. Tow elements with the same value get the same rank, equal to the average of the rank had the elements different values.
• TreeCluster (int,char,double[][],ref int[,], ref double[]) - calls the clustering method
• PalCluster (int,dobule[][],int[,],double[]) - performs clustering using pairwise average linkage on the given distance matrix
• PslCluster (int,dobule[][],int[,],double[]) - performs clustering using pairwise single linkage on the given distance matrix
• PmlCluster (int,dobule[][],int[,],double[]) - performs clustering using pairwise complete(maximum) linkage on the given distance matrix
• HierarchiclCluster (string,int) - save clustering resuls (.gtr or .atr files)

Private Members

• char geneMatric - distance method to be used in calculating genes
• char arrayMatric - distancd method to be used in calculating arrays (samples)
• char method - hierarchical clustering algorithm to be used
• string filename - file name to load
• string pathName - a location that different from original path
• int partoalRowNum - number of rows to load