tests/testthat/test_functions.R

In pagoda2: Single Cell Analysis and Differential Expression

library(pagoda2)
library(dplyr)

test_that("namedNames() functionality", {
    expect_equal(namedNames(c(1, 2, 3)), NULL)
})


test_that("check cm dims", {
	## We have pre-generated a dataset of 50 bone marrow cells that you can load as a matrix directly
    cm <- readRDS(system.file("extdata", "sample_BM1_50.rds", package="pagoda2"))
    expect_equal(dim(cm)[1], 33694)
    expect_equal(dim(cm)[2], 50)
})


test_that("check basic qc of counts", {
	## remove two cells
    cm <- readRDS(system.file("extdata", "sample_BM1_50.rds", package="pagoda2"))
    counts <- gene.vs.molecule.cell.filter(cm, min.cell.size=500)
    expect_equal(dim(counts)[1], 33694)
    expect_equal(dim(counts)[2], 50)
    ## Filter and check the size of the resulting matrix:
    counts <- counts[rowSums(counts)>=10,]
    expect_equal(dim(counts)[1], 1432)
    expect_equal(dim(counts)[2], 50)
})