In jakobwalter/RNAPerm: Testing Differential Expression using Permutation Tests

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(RNAPerm)

n <- 12
p <- 10
Y <- rnbinom(n*p, mu = 10, size = 1/0.2)
Y <- data.frame(array(Y, dim = c(n, p)))
X1 <- as.factor(rep(c("A", "B"), each = n/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)
pMWU     <- classicPermTest(dge, design, 200)
pFlipScoresBasic <- flipScoresTest(dge, design, scoreType = "basic", toBeTested = 2)
pFlipScoresEffective <- flipScoresTest(dge, design, scoreType = "effective", toBeTested = 2)

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