tests/testthat/testmotif.R

In motifcounter: R package for analysing TFBSs in DNA sequences

context("Motif tests")

test_that("motif validity",
{
    # Read motif
    motiffile=system.file("extdata","x1.tab", package="motifcounter")
    motif=t(as.matrix(read.table(motiffile)))
    motifValid(motif)

    # not a matrix
    expect_error(motifValid("hallo"))

    #wrong dimensionality
    expect_error(motifValid(t(motif)))

    # provoke wrong nomalization
    motif[1,1]=0
    expect_error(motifValid(motif))
    
    # renormalize to solve the issue
    motifValid(normalizeMotif(motif))
    
    # provoke wrong nomalization
    motif[1,1]=.1
    expect_error(motifValid(motif))

    # renormalize to solve the issue
    motifValid(normalizeMotif(motif))

    # test reverse complement
    expect_equal(as.vector(motif), as.vector(revcompMotif(revcompMotif(motif))))
})