tests/testthat/setup.R

In LTLA/GenomicInteractions: Classes and Methods for Handling Genomic Interaction Data

# library(testthat); library(GenomicInteractions)

chrlens <- c(chrA=1000, chrB=2000)
chromos <- names(chrlens)

spawn_gi <- function(N1=30, N2=15, Np=50) {
    all.starts <- round(runif(N1, 1, 100))
    all.ends <- all.starts + round(runif(N1, 5, 20))
    regions1 <- GRanges(sample(chromos, N1, replace=TRUE), IRanges(all.starts, all.ends), seqlengths=chrlens)
    regions1 <- unique(regions1)

    all.starts <- round(runif(N2, 1, 100))
    all.ends <- all.starts + round(runif(N2, 5, 20))
    regions2 <- GRanges(sample(chromos, N2, replace=TRUE), IRanges(all.starts, all.ends), seqlengths=chrlens)
    regions2 <- unique(regions2)

    Np <- 20
    all.anchor1 <- sample(length(regions1), Np, replace=TRUE)
    all.anchor2 <- sample(length(regions2), Np, replace=TRUE)
    GenomicInteractions(Factor(levels=regions1, index=all.anchor1), Factor(levels=regions2, index=all.anchor2))
}

spawn_regions <- function(Ngenes=10) {
    gene.starts <- round(runif(Ngenes, 1, 100))
    gene.ends <- gene.starts + round(runif(Ngenes, 5, 20))
    gene.strand <- sample(c("*", "+", "-"), Ngenes, replace=TRUE)
    GRanges(sample(chromos, Ngenes, replace=TRUE), IRanges(gene.starts, gene.ends), 
        strand=gene.strand, seqlengths=chrlens)
}

expect_as_if <- function(x, y) {
    expect_identical(unfactor(first(x)), unfactor(first(y)))
    expect_identical(unfactor(second(x)), unfactor(second(y)))
    expect_identical(mcols(x), mcols(y))
    expect_identical(metadata(x), metadata(y))
    expect_identical(names(x), names(y))
}