inst/unitTests/test_ensdb.R

In jotsetung/biovizBase: Basic graphic utilities for visualization of genomic data.

## Simple test function to test the crunch method on EnsDb
library(EnsDb.Hsapiens.v75)
edb <- EnsDb.Hsapiens.v75

test_crunch_ensdb <- function(){
    zbtb <- genes(edb, filter = ~ genename == "ZBTB16")

    Zens <- crunch(edb, zbtb)
    checkTrue(all(Zens$gene_name == "ZBTB16"))
    ## Expect a single gene.
    checkEquals(length(unique(Zens$gene_id)), 1)
    ## crunch without which but using a filter.
    Test <- crunch(edb, ~ genename == "ZBTB16")
    checkEquals(Zens, Test)

    ## Testing exceptions:
    checkException(crunch(edb, which = "bla"))

    strand(zbtb) <- "*"
    ## Expect two genes.
    Test <- crunch(edb, zbtb)
    checkEquals(length(unique(Test$gene_id)), 3)

    ## Testing columns
    wantCols <- c("gene_biotype", "tx_biotype")
    Test <- crunch(edb, zbtb, columns = wantCols)
    checkTrue(all(wantCols %in% colnames(mcols(Test))))

    ## Now let's try a tricky one...
    Test <- crunch(edb, which = GenenameFilter("ALDOA"))
    gr <- GRanges(seqnames = 16, IRanges(30768000, 30770000), strand = "*")
    Test <- crunch(edb, which = gr)
}