```
## Running CRE
runCRE <- function(npp, npm, npz, nmp, nmm, nmz, nrp, nrm, nrz, nzp, nzm, nzz, method = c("Ternary","Quaternary","Enrichment","Fisher"))
{
method = match.arg(method)
if(method == 'Quaternary'){
qR = nrp + nrm + nrz
qZero = nzp + nzm + nzz
nPlus = npp + nmp + nrp + nzp
nMinus = npm + nmm + nrm + nzm
nZero = npz + nmz + nrz + nzz
## Assume up-regulated
qPlus = npp + npm + npz
qMinus = nmp + nmm + nmz
score = npp + nmm + nrp + nrm - (npm + nmp)
pval.up = QP_Pvalue(score = score, q_p = qPlus, q_m = qMinus, q_z = qZero,
q_r = qR, n_p = nPlus, n_m = nMinus, n_z = nZero)
## Assume down-regulated
qPlus = nmp + nmm + nmz
qMinus = npp + npm + npz
score = nmp + npm + nrp + nrm - (npp + nmm)
pval.down = QP_Pvalue(score = score, q_p = qPlus, q_m = qMinus, q_z = qZero,
q_r = qR, n_p = nPlus, n_m = nMinus, n_z = nZero)
} else if (method == 'Ternary'){
qR = 0
qZero = nzp + nzm + nzz
nPlus = npp + nmp + nzp
nMinus = npm + nmm + nzm
nZero = npz + nmz + nzz
## Assume up-regulated
qPlus = npp + npm + npz
qMinus = nmp + nmm + nmz
score = npp + nmm - (npm + nmp)
pval.up = QP_Pvalue(score = score, q_p = qPlus, q_m = qMinus, q_z = qZero,
q_r = qR, n_p = nPlus, n_m = nMinus, n_z = nZero)
## Assume down-regulated
qPlus = nmp + nmm + nmz
qMinus = npp + npm + npz
score = nmp + npm - (npp + nmm)
pval.down = QP_Pvalue(score = score, q_p = qPlus, q_m = qMinus, q_z = qZero,
q_r = qR, n_p = nPlus, n_m = nMinus, n_z = nZero)
} else if (method == 'Enrichment'){
nrp = npp + nmp + nrp
nrm = npm + nmm + nrm
nrz = npz + nmz + nrz
qPlus = 0
qMinus = 0
qR = nrp + nrm + nrz
qZero = nzp + nzm + nzz
nPlus = nrp + nzp
nMinus = nrm + nzm
nZero = nrz + nzz
score = nrp + nrm
pval.up = QP_Pvalue(score = score, q_p = qPlus, q_m = qMinus, q_z = qZero,
q_r = qR, n_p = nPlus, n_m = nMinus, n_z = nZero)
pval.down = pval.up
} else if (method == 'Fisher'){
nrp = npp + nmp + nrp
nrm = npm + nmm + nrm
nrz = npz + nmz + nrz
M = matrix(0, nrow = 2, ncol = 2)
M[1,1] = nrp + nrm
M[1,2] = nrz
M[2,1] = nzp + nzm
M[2,2] = nzz
pval.up = fisher.test(M, alternative = 'greater')$p.val
pval.down = pval.up
}
pval = list(pval.up = pval.up, pval.down = pval.down)
pval
}
```

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