tests/testthat/test_sparseHiC.R

In aryeelab/sparseHiC: Efficient compression and analysis of Hi-C Data

context("Basic Hi-C Pro impot works")

test_that("We get a list of 23 chromosomes and the matrix is square for chromosome 1", {
    matrix.file <- paste(system.file("extdata", package = "processedHiCdata"),
                          "HiC-Pro/hESC_Rep1/hESC_Rep1_1000000_iced.matrix", sep = "/")
    bed.file <- paste(system.file("extdata", package = "processedHiCdata"),
                      "HiC-Pro/hESC_Rep1/hESC_Rep1_1000000_abs.bed", sep = "/")
    genomeBuild <- "hg19"
    res <- "1000000"
    sampleName <- "hESC1"
    x <- import.HiCPro(matrix.file, bed.file, res, sampleName, genomeBuild)
    expect_equal(length(x@resolutionNamedList), 1)
    expect_equal(length(x@resolutionNamedList[[1]]), 23)
    expect_equal(dim(x@resolutionNamedList[[1]][[1]])[1], dim(x@resolutionNamedList[[1]][[1]])[2])
    expect_equal(dim(x@resolutionNamedList[[1]][[1]])[1], 250)
})

context("Primitive Sample Addition")

test_that("Associative and commutative properties of S4 data holds", {
    rdsA<-paste(system.file('rds',package='sparseHiC'),'hESCdatum1.rds',sep='/')
    hESCdatum1 <- readRDS(rdsA)
    rdsB<-paste(system.file('rds',package='sparseHiC'),'hESCdatum2.rds',sep='/')
    hESCdatum2 <- readRDS(rdsB)
    rdsC<-paste(system.file('rds',package='sparseHiC'),'IMR90datum1.rds',sep='/')
    IMR90datum1 <- readRDS(rdsC)
    hESCdata <- hESCdatum1 + hESCdatum2
    threeA <- IMR90datum1 + hESCdata
    threeB <-  IMR90datum1 + hESCdatum1 + hESCdatum2
    expect_equal(threeA, threeB)
    expect_equal(utils::object.size(IMR90datum1 + hESCdatum1 + hESCdatum2),
                 utils::object.size(hESCdatum1 + hESCdatum2 + IMR90datum1))
})