library(Rinbix)
data(simrnaseq)
context("RNA-Seq")
test_that("DESeq", {
require(DESeq)
data(simrnaseq)
X <- t(predictorsTrain)
y <- as.factor(responseTrain - 1)
rDeseq <- rankDeseq(X, y)
expect_equal(nrow(rDeseq), ncol(predictorsTrain))
})
test_that("DESeq2", {
require(DESeq2)
data(simrnaseq)
X <- t(predictorsTrain)
y <- as.factor(responseTrain - 1)
rDeseq2 <- rankDeseq2(X, y)
expect_equal(nrow(rDeseq2), ncol(predictorsTrain))
})
test_that("edgeR", {
require(edgeR)
data(simrnaseq)
X <- t(predictorsTrain)
y <- as.factor(responseTrain - 1)
rEdger <- rankEdgeR(X, y)
expect_equal(nrow(rEdger), ncol(predictorsTrain))
})
test_that("edgeR GLM", {
require(edgeR)
data(simrnaseq)
X <- t(predictorsTrain)
y <- as.factor(responseTrain - 1)
covars <- rnorm(ncol(X))
rEdgerGlm <- rankEdgeRGlm(X, y, covars)
expect_equal(nrow(rEdgerGlm), ncol(predictorsTrain))
})
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