tests/testthat/test_genesList_c.R

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

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

#load genetic_data
genedata <- readRDS("genetic_data.rds")

MAE <- MultiAssayExperiment(list("genedata" = genedata))

#perform GenesList combined function
MAE <- genesList(MAE, method = 'c',
                 genetic_data = assay(MAE, 1),
                 timeString = 'D')

#internal checks
G <- assay(MAE, 1)

colnames(G) <- gsub(x = colnames(G), pattern = 'D', replacement = 'TP')

#check1
#genetic_data should not have 'D' in the colnames
test_that("genetic_data colnames has not 'D' in it", {
    for (i in 1:10) {
        expect_false(grepl(colnames(G), pattern = 'D')[i])
    }
})

#continue
X <- lapply(split.default(G, sub("(TP\\d+).*","\\1", names(G))), as.list)

#check 2
#should be a list of 5 lists
test_that("X is a list of 5", {
    expect_equal(length(X), 5)
})

#continue
names(X) <- gsub(names(X), pattern = 'TP', replacement = 'D')

#check 3
#there should be 'D' in list names
test_that("genetic_data colnames has not 'D' in it", {
    for (i in 1:5) {
        expect_true(grepl(names(X), pattern = 'D')[i])
    }
})

#continue
L1 <- lapply(X, data.frame, stringsAsFactors = FALSE)

L2 <- lapply(L1, function(DF) {rownames(DF) <- rownames(assay(MAE, 1)); DF})

#check 4
#nested DFs in L2 have the same rownames as genetic_data
test_that("Dfs in L2 have the same rownames as in genetic_data", {
    a <- lapply(L2, function(x) { rownames(x)})
    for (i in 1:5) {
        expect_equal(as.character(unlist(a[i])), as.character(rownames(G)))
    }
})

#continue
C1 <- gtools::mixedsort(names(L2))

L2 <- L2[C1]

L3 <- L2[gtools::mixedsort(names(L2))]

genelist_man <- lapply(L3, function(x) {
    colnames(x) <- sub(x = colnames(x), pattern = 'TP', replacement = 'D')
x}
)

metadata(MAE)[["genelist_man"]] <- genelist_man

#check 5
#are genelist_man and genelist the same?
test_that("manual and function output is the same", {
    expect_equal(metadata(MAE)[["geneslist"]], metadata(MAE)[["genelist_man"]])
})

#savedata
saveRDS(metadata(MAE)[[1]],"geneslist_c.rds", compress = "xz")