inst/unitTests/test_FieldEffectCrc.R

In BarcUVa-Seq/FieldEffectCrc: Tumor, tumor-adjacent normal, and healthy colorectal transcriptomes as SummarizedExperiment objects

test_cohortB <- function() {
    hub <- ExperimentHub::ExperimentHub()
    r <- AnnotationHub::query(hub, c("FieldEffectCrc"))
    se <- r[["EH3525"]]
    RUnit::checkEquals(dim(se)[1], 37361)
    RUnit::checkEquals(dim(se)[2], 30)
}

test_make_txi <- function() {
    hub <- ExperimentHub::ExperimentHub()
    r <- AnnotationHub::query(hub, c("FieldEffectCrc"))
    se <- r[["EH3525"]]
    txi <- make_txi(se)
    RUnit::checkEquals(is(txi)[1], "list")
}

test_reorder_assays <- function() {
    hub <- ExperimentHub::ExperimentHub()
    r <- AnnotationHub::query(hub, c("FieldEffectCrc"))
    se <- r[["EH3525"]]
    se <- reorder_assays(se)
    RUnit::checkEquals(names(SummarizedExperiment::assays(se))[1], "counts")
}