Different p-values are produced for each gene set using a different statistical procedure and a randomization distribution. The p-values obtained are used to test the self-contained hypothesis of gene set diffferential expression

marginal.analysis(df, y, test, orness, nsim = 100, method = "dbinom",
  type = "within-pair", is.decreasing = FALSE, to.save = FALSE,
  foutput = "marginal.analysis.rda")

Arguments

df

Count matrix

y

Vector giving the pairs of columns

test

Function comparing counts within each pair

orness

Orness

nsim

Number of simulations

method

Method to generate the orness values. See owa.weights.

type

Randomization distribution to generate random pairs

is.decreasing

The values to aggregated should decreasing ordered

to.save

Is to be saved in foutput?

foutput

Output file