inst/tests/test-annotateChromosome.R

In lianos/GenomicCache: Support package for GenomicFeatures

################################################################################
## Test data
clengths <- c(chr1=10000, chr2=5000)
chr1 <- factor('chr1', levels=c('chr1', 'chr2'))
chr2 <- factor('chr2', levels=c('chr1', 'chr2'))
g1 <- GRanges(seqname=chr1,
              ranges=IRanges(c(10, 40, 80, 120), width=21),
              strand='+',
              seqlengths=clengths)
values(g1) <- DataFrame(exon.anno=c('utr5', 'cds', 'cds', 'utr3'))

g2 <- GRanges(seqname=chr1,
              ranges=IRanges(c(200, 250, 300, 400), width=31),
              strand='+',
              seqlengths=clengths)
values(g2) <- DataFrame(exon.anno=c('utr5', 'cds', 'cds', 'utr3'))

## First exon overlaps with parts of exons 2,3 in g1
## Secon exon is in intron 3
o1 <- GRanges(seqname=chr1,
              ranges=IRanges(start=c(50, 105), end=c(85, 115)),
              strand='+',
              seqlengths=clengths)
values(o1) <- DataFrame(exon.anno=c('cds', 'cds'))

g3r <- GRanges(seqnames=chr1,
               ranges=IRanges(start=c(15, 50), end=c(45, 100)),
               strand='-',
               seqlengths=clengths)
values(g3r) <- DataFrame(exon.anno=c('cds', 'utr5'))

gchr1 <- GRangesList(GeneA=g1, GeneB=g2, GeneC=o1, GeneD=g3r)
lchr1 <- list(GeneA=g1, GeneB=g2, GeneC=o1, GeneD=g3r)

anno.stranded <- annotateChromosome(lchr1, flank.up=2, flank.down=5, 'chr1',
                                    clengths[['chr1']], stranded=TRUE)
## anno.nostrand <- annotateChromosome(lchr1, flank.up=2, flank.down=5, 'chr1',
##                                     clengths[['chr1']],stranded=FALSE)
################################################################################
## Run tests
context("Annotate Chromosome")
test_that("No regions on annotated chromosome overlap", {
  o <- findOverlaps(anno.stranded, ignoreSelf=TRUE, type='any')
  expect_that(length(o), equals(0))
})

test_that("Chromosome is annotated", {

})

test_that("overlaps do not overlap with eachother, or other annotations ..", {
  ## stranded.over <- anno.stranded[values(anno.stranded)$exon.anno == 'overlap']
  ## for (ostrand in unique(as.character(strand(stranded.over)))) {
  ##   so <- stranded.over[strand(stranded.over) == ostrand]
  ##   o <- findOverlaps(ranges(so), ignoreSelf=TRUE, type='any')
  ##   expect_that(length(o), equals(0L),
  ##               info="overlap annotations do not overlap")

  ## }
})