classicPermTest: Classic Permutation Test for RNA-Seq Data

In jakobwalter/RNAPerm: Testing Differential Expression using Permutation Tests

Classic Permutation Test for RNA-Seq Data

Description

Computes p-values using a classic permutation test based on the absolute difference in means.

Usage

classicPermTest(dge, design, nPerm)

Arguments

dge	A dgeList object, created with edgeR, containing the normalization factors as computed by edgeR.
design	A model matrix; The first column should be all 1s. The second column should have two unique values, corresponding to the groups
nPerm	Number of random permutations used for the computation of the p-value

Author(s)

Jakob Walter

References

Hemerik, Jesse, and Jelle Goeman. "Exact testing with random permutations." Test 27.4 (2018): 811-825.

Examples

Y <- rnbinom(20*10, mu = 10, size = 1/0.2)
Y <- data.frame(array(Y, dim = c(20, 10)))
X1 <- as.factor(rep(c("A", "B"), each = 20/2))
design <- model.matrix(~X1, contrasts.arg = list(X1 = "contr.sum"))
dge <- edgeR::DGEList(counts = t(Y), group = X1)
dge <- edgeR::calcNormFactors(dge)
pClassic <- classicPermTest(dge, design, 200)

jakobwalter/RNAPerm documentation built on Sept. 17, 2022, 3:57 p.m.