# simple example of the use of  SAM

# twoclass (unpaired) example

set.seed(100)
x<-matrix(rnorm(1000*20),ncol=20)
dd<-sample(1:1000,size=100)

u<-matrix(2*rnorm(100),ncol=10,nrow=100)
x[dd,11:20]<-x[dd,11:20]+u

y<-c(rep(1,10),rep(2,10))

data=list(x=x,y=y, geneid=as.character(1:nrow(x)),genenames=paste("g",as.character(1:nrow(x)),sep=""), logged2=T)

params=list(min.foldchange=0)

#params=list(min.foldchange=1.5)

a<-samr(data, params, resp.type="twoclass", nperm=50)


# makes sam plot- also returns info needed to make this plot in Excel

pp=samr.plot(a,.4, params)


# make delta and significant genes tables

delta.table <- samr.compute.delta.table(a, params)

siggenes.table <- samr.compute.siggenes.table(a,del, data, delta.table, params)


## note, fo delta slider, precompute things first via samr.compute.delta.table