# 07 January 2010
library(hopach)
#mydata <- read.table(file="/Users/grobertson/GENEREG/ChIP/CHIP_SEQ/SOLEXA/TCGA/external_data/DNA_methylation/xhost09/matrix.for-clustering.txt", header = TRUE, row.names = 1, sep="\t")
data <- read.table(file="/Users/grobertson/GENEREG/ChIP/CHIP_SEQ/SOLEXA/TCGA/external_data/DNA_methylation/xhost09/LAML.matrix.for-clustering.20110107.head-n2000.txt", header = TRUE, row.names = 1, sep="\t")
dim(mydata)
mydist <-distancematrix( mydata, d="cosangle" )
gene.hobj <- hopach(data,dmat=mydist)