justDo2.Rd
Function to simulation study
justDo2(n, N, nsig, noutlier = c(1, 1), theta, model = c("Poisson", "NB"), test = proportion.p, norness = 50, nsim = 100, method = "dbinom", is.decreasing = FALSE, proc = c("owb", "owc", "er", "de"), do.auc = FALSE)
n | Number of pairs |
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N | Number of genes |
nsig | Number of significant genes (rows (noutlier+1):(noutlier+nsig) |
noutlier | Vector giving the number of outlier genes noutlier[1] (rows 1:noutlier[1] in the expression matrix) and number of pairs (columns 1:noutlier[2]) |
theta | Vector with the lambda values for tami::rPairedPoisson or matrix with two columns and 4 rows where the entry theta[i,1] is the mean and 1/theta[i,2] the dispersion for the i-th random variable |
model | Distribution of the random counts: "Poisson" or "NB" for Poisson or negative binomial distribution |
test | Function comparing counts within each pair |
norness | Number of values for orness if orness == NULL |
nsim | Number of simulations |
method | Method to generate the orness values
|
is.decreasing | The values to be aggregated in decreasing order |
proc | Procedures to be tested: |
do.auc | Is the AUC value to be calculated? |