Function to simulation study

justDo(n, N, nsig, noutlier = c(1, 1), lambda, test = proportion.p,
  norness = 50, nsim = 100, method = "dbinom", type = "complete",
  is.decreasing = FALSE, proc = c("owb", "owc", "er", "de"),
  do.auc = FALSE)

Arguments

n

Number of pairs

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])

lambda

Vector with the lambda values for tami::rPairedPoisson

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 c("dbinom","fuller"). See owa.weights.

type

Randomization distribution to generate random pairs

is.decreasing

The values to be aggregated in decreasing order

proc

Procedures to be tested: owb OWA with between-pair distribution, owc OWA with complete distribution, er edgeR, de DESEq2.

do.auc

Is the AUC value to be calculated?