/TJPROJ6/RNA_SH/personal_dir/zhanghailei/script/maSigPro
<code>

library(maSigPro)
#data(data.abiotic)

#data(edesign.abiotic)
edesign.abiotic <- read.table(file="co1n.txt",header=TRUE,sep="\t",row.names= 1)
data.abiotic <- read.table(file="fpkm.txt",header=TRUE,sep="\t",row.names= 1)

##########################

design <- make.design.matrix(edesign.abiotic, degree = 2)
########cha yi fen xi #######
fit <- p.vector(data.abiotic, design, Q = 0.05, MT.adjust = "BH")

##########

tstep <- T.fit(fit, step.method = "backward", alfa = 0.05)

#######################

sigs <- get.siggenes(tstep, rsq = 0.6, vars = "groups")

# design$groups.vector

p <- see.genes(sigs$sig.genes$Control, show.fit = T, dis =design$dis, cluster.method="hclust" ,cluster.data = 1, k = 9)
#pdf('maSigPro.pdf')
#p
#dev.off()
for (i in 1:length(p$cut)){
     fname <- paste('subcluster_', p$cut[[i]], sep='')
     write.table(p$cut[i], file=fname, quote=F, sep='\t', col.names=F,append=T)
     }

</code>