tests/testthat/test-GetCellMat.R

In scCB2: CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data

data(mbrainSub)
library(SummarizedExperiment)

mbrainReal <- mbrainSub[, Matrix::colSums(mbrainSub) > 500]
CBOut <- SummarizedExperiment(
    list(cell_matrix = mbrainReal[,sample(ncol(mbrainReal), 
                                          200, replace = TRUE)]))

test_that("Output matrix format", {
    expect_identical(class(GetCellMat(CBOut)), class(assay(CBOut)))
})

test_that("Mitochondrial filtering", {
    expect_error(GetCellMat(CBOut, MTgene = "1"),
                 "invalid character indexing")
    expect_error(GetCellMat(CBOut, MTfilter = -1), "between 0 and 1")
    
    MTgene <- sample(rownames(assay(CBOut)), 10)
    for (k in c(0.5, 0.1, 0.01, 0.001, 0)) {
        CBMat <- GetCellMat(CBOut, k, MTgene)
        MTprop <-
            Matrix::colSums(CBMat[MTgene, ]) / Matrix::colSums(CBMat)
        expect_true(all(MTprop <= k))
    }
})