calcRss: Function calculates the average RSS for a set of cluster...

In jmarlab/attract: Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

Description

Function calculates the average RSS for a set of cluster assignments.

Usage

calcRss(exprs.dat, cl, class.vector)

Arguments

exprs.dat	a matrix of gene expression values.
cl	a vector of cluster assignments.
class.vector	a vector specifying the group membership of the samples.

Details

This function is called internally by findSynexprs. For an informative cluster, the RSS values should be very small relative to those produced by the informativeness metric (the MSS values).

Value

A numeric value representing the average RSS value for this set of cluster assignments.

Author(s)

Jessica Mar

Examples

## Not run: 
library(cluster)
data(subset.loring.eset)
clustObj <- agnes(as.dist(1-t(cor(exprs(subset.loring.eset)))))
crss.vals <- NULL 
for( i in 1:10 ){
	crss.vals <- c(crss.vals, calcRss(exprs(subset.loring.eset), cutree(clustObj,i), pData(subset.loring.eset)$celltype))
}
# The RSS values are expected to be smaller than the informativeness metric values in the presence of genuine cluster structure.

## End(Not run)

jmarlab/attract documentation built on May 23, 2019, 9:02 p.m.