tree.weight {mdw} | R Documentation |
Weights based on GSC Tree Method
Description
tree.weight
Produce a set of weights for different end points based on a correlation matrix using the GSC tree method
Usage
tree.weight (cor.mat, method="GSC", clustering.method="average", plot=TRUE,
orientation=c("vertical","horizontal"), ...)
Arguments
cor.mat |
a matrix, correlation matrix |
method |
a string. GSC, implementation of Gerstein et al., is the only implemented currently |
clustering.method |
a string, how the bottom-up hierarchical clustering tree is built, is passed to hclust as the method parameter |
plot |
a Boolean, whether to plot the tree |
orientation |
vertical or horizontal |
... |
additional args |
Value
A vector of weights that sum to 1.
Author(s)
Youyi Fong yfong@fhcrc.org
References
Gerstein, M., Sonnhammer, E., and Chothia, C. (1994), Volume changes in protein evolution. J Mol Biol, 236, 1067-78.
Examples
cor.mat=diag(rep(1,3))
cor.mat[1,2]<-cor.mat[2,1]<-0.9
cor.mat[1,3]<-cor.mat[3,1]<-0.1
cor.mat[2,3]<-cor.mat[3,2]<-0.1
tree.weight(cor.mat)
[Package mdw version 2020.6-17 Index]