tests/testthat/test_annotateTiles.R

In MOCHA: Modeling for Single-Cell Open Chromatin Analysis

if (requireNamespace("org.Hs.eg.db", quietly = TRUE) &&
  requireNamespace("TxDb.Hsapiens.UCSC.hg38.refGene", quietly = TRUE) &&
  requireNamespace("TxDb.Hsapiens.UCSC.hg19.knownGene", quietly = TRUE)) {
  test_that("annotateTiles works on a 1 sample test dataset", {
    cellPopulations <- c("C2", "C5")
    capture.output(
      SampleTileMatrix <- MOCHA::getSampleTileMatrix(
        MOCHA:::testTileResults,
        cellPopulations = cellPopulations,
        threshold = 0
      ),
      type = "message"
    )

    capture.output(
      STM <- MOCHA::annotateTiles(SampleTileMatrix,
        promoterRegion = c(2000, 100)
      ),
      type = "message"
    )

    expect_snapshot(
      SummarizedExperiment::rowRanges(STM),
      variant = "1sample"
    )
  })

  test_that("annotateTiles works on a 3 sample test dataset", {
    cellPopulations <- c("C2", "C3")
    capture.output(
      SampleTileMatrix <- MOCHA::getSampleTileMatrix(
        MOCHA:::testTileResultsMultisample,
        cellPopulations = cellPopulations,
        threshold = 0
      ),
      type = "message"
    )

    capture.output(
      STM <- MOCHA::annotateTiles(SampleTileMatrix,
        promoterRegion = c(2000, 100)
      )
    )

    expect_snapshot(
      SummarizedExperiment::rowRanges(STM),
      variant = "3sample"
    )
  })


  test_that("annotateTiles works on a GRanges", {
    require(TxDb.Hsapiens.UCSC.hg38.refGene)
    require(org.Hs.eg.db)
    cellPopulations <- c("C2", "C3")
    capture.output(
      SampleTileMatrix <- MOCHA::getSampleTileMatrix(
        MOCHA:::testTileResultsMultisample,
        cellPopulations = cellPopulations,
        threshold = 0
      ),
      type = "message"
    )
    capture.output(
      ranges <- MOCHA::annotateTiles(SummarizedExperiment::rowRanges(SampleTileMatrix),
        TxDb = TxDb.Hsapiens.UCSC.hg38.refGene,
        Org = org.Hs.eg.db,
        promoterRegion = c(2000, 100)
      ),
      type = "message"
    )

    expect_snapshot(
      ranges,
      variant = "3sample"
    )
  })
}