EBSeqTest <- function(data,conditions,uc, AllParti=NULL, iLabel = 1,sizefactor = 1,
iter = 50,alpha = 0.4, beta = 0, step1 = 1e-6,step2 = 0.01,
thre = log(2), sthre = 0.001, filter = 10, stopthre = 1e-3, nequal = 2) {
if(!is.matrix(data))
{
stop("data must be a numerical matrix")
}
if(length(conditions) != ncol(data))
{
stop("incorrect length of conditions")
}
if(length(beta) > 1)
{
if(length(beta) != nrow(data)){stop("incorrect length of hyper parameters")}
}
if(beta == 0)
{
beta = rep(2,nrow(data))
}
if(length(iLabel) == 1 && iLabel == 1)
{
iLabel = 1:nrow(data)
}
if(length(iLabel) != nrow(data))
{
stop("incorrect length of isoform label")
}
if(length(sizefactor) == 1 && sizefactor == 1)
{
sizefactor = rep(1,ncol(data))
}
if(length(sizefactor) != ncol(data))
{
stop("incorrect length of size factor")
}
if(is.null(AllParti)){
AllParti = matrix(0,nrow=1,ncol=length(levels(conditions)))
}
.Call('EBSeq',
scExpMatrix = data,
groupLabel = conditions,
AllParti = AllParti,
iLabel = iLabel,
sizeFactor = sizefactor,
iter = iter,
alpha = alpha,
beta = beta,
step1 = step1,
step2 = step2,
uc = uc,
thre = thre,
sthre = sthre,
filter = filter,
stopthre = stopthre,
nequal = nequal)
}
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