tests/testthat/test_combineGenes.R

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

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

#get data sorted
MAE <- readRDS("MAE_mm.rds")

miR <- assay(MAE, 1)[1:100,]

mRNA <- assay(MAE, 2)[1:200,]

MAE2 <- MultiAssayExperiment(list("miR2" = miR, "mRNA2" = mRNA))

MAE <- c(MAE, MAE2)

#test combineGenes function
MAE <- combineGenes(MAE, miR_data = assay(MAE, 3), mRNA_data = assay(MAE, 4))

#internal tests
miR_data <- assay(MAE, 3)

mRNA_data <- assay(MAE, 4)

miR_order <- gtools::mixedsort(names(miR_data))

mRNA_order <- gtools::mixedsort(names(mRNA_data))

#check 1
#column names in miRs and mRNAs are the same
test_that("Column names are named as expected", {
    expect_equal(as.character(names(assay(MAE, 1))),
    as.character(names(assay(MAE, 2))))
})

#continue
miR_data <- assay(MAE, 3)[miR_order]

mRNA_data <- assay(MAE, 4)[mRNA_order]

genetic_data_manual <- rbind(miR_data, mRNA_data)

# external check
#check rowsums of genetic_data_man and genetic_data
test_that("function and manual outcomes are the same", {
    expect_equal(length(rownames(genetic_data_manual)),
    length(rownames(assay(MAE, 3))) + length(rownames(assay(MAE, 4))))
})

#save data
saveRDS(assay(MAE, 5), "genetic_data.rds", compress = "xz")