gcc.dist: compute distance matrix for hierarchical clustering

In rsgcc: Gini methodology-based correlation and clustering analysis of microarray and RNA-Seq gene expression data

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.

Author(s)

Chuang Ma, Xiangfeng Wang

See Also

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

Examples

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

rsgcc documentation built on May 2, 2019, 9:25 a.m.