rsgcc (version 1.0.6)

gcc.dist: compute distance matrix for hierarchical clustering

Description

This function computes the distance between the rows of a data matrix with the specified distance method.

Usage

gcc.dist(x, 
      cpus = 1,
      method = c("GCC", "PCC", "SCC", "KCC", "BiWt", "MI", "MINE", "ED"),
      distancemethod = c("Raw", "Abs", "Sqr"))

Arguments

x

a data matrix containing numeric variables, which is the same as the "GEMatrix" defined in the cor.matrix function.

cpus

the number of cpus used for computation.

method

a character string indicating the method to be used to calculate the associations.

distancemethod

a character string indicating the distance method to be used. Currently, three distance methods are available, include: "Raw" (1-cor)", "Abs" (1-|cor|), and "Sqr" (1-|cor|^2).

Value

• A list with the following components:
• dist
  a data matrix containing the distances between different genes.
• pairmatrix
  a data matrix including the correlation between different genes.

See Also

cor.matrix, gcc.hclust, gcc.tsheatmap.

Examples

data(rsgcc)
   x <- rnaseq[1:10,]
   gcc.dist(x, method = "GCC", distancemethod = "Raw", cpus = 1)