tests/testthat/test_diffExpressRes.R

In Krutik6/TimiRGeN: Time sensitive microRNA-mRNA integration, analysis and network generation tool

#devtools::uses_testthat()
library(TimiRGeN)
library(testthat)

#load data
#format miR and mRNA data
#load ID data
MAE <- readRDS("MAE_mm.rds")

miR <- readRDS("IDs_mouse_miR.rds")

mRNA <- readRDS("IDs_mouse_mRNA.rds")

#test function
MAE <- diffExpressRes(MAE, df = assay(MAE, 2), dataType = 'Log2FC',
                       genes_ID = assay(mRNA, 1),
                       idColumn = 'GENENAME',
                       'mRNA_log2fc')

#internal checks on mRNA data
exp <- cbind(names = rownames(assay(MAE, 2)),
             assay(MAE, 2)[,grep('Log2FC', colnames(assay(MAE, 2)))])

#check 1
#exp should be the same row length as mRNA
test_that("aspects of exp should be similar to mRNA", {
    expect_equal(length(rownames(assay(MAE, 2))), length(rownames(exp)))
    expect_equal(rownames(assay(MAE, 2)), rownames(exp))
})

#continue
merged <- merge(exp, mRNA@ExperimentList$mRNA_entrez, by.x = 'names',
                by.y = 'GENENAME',all = TRUE)

rownames(merged) <- merged[[1]]

merged[[1]] <- NULL

#check 2
#functional and manual output should be the same
test_that("output is the same in merged and mRNA_log2fc", {
    expect_equal(merged, assay(MAE, 3))
})

#Express on miRNA data
MAE <- diffExpressRes(MAE, df = assay(MAE, 1),
                    dataType = 'Log2FC',
                    genes_ID = assay(miR, 3),
                    idColumn = 'GENENAME',
                    name = 'miR_log2fc')

#save data as rds
saveRDS(MAE, "log2fc.rds", compress = "xz")