tests/testthat/test-determineProteotypicFragments.R

In ErasmusMC-CCBC/ProteoDisco: Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences

# context("Determination and incorporation of proteotypic fragments")
#
# test_that("Proteotypic fragments can be determined and incorporated", {
#
#     # Import example ProteoDiscography (hg19)
#     data('ProteoDiscographyExample.hg19', package = 'ProteoDisco')
#     ProteoDiscographyExample.hg19 <- ProteoDisco::setTxDb(ProteoDiscographyExample.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene)
#     ProteoDiscographyExample.hg19 <- ProteoDisco::setGenomicSequences(ProteoDiscographyExample.hg19, BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19)
#
#     # Check proteotypic fragments.
#     ProteoDiscographyExample.hg19 <- ProteoDisco::checkProteotypicFragments(
#         ProteoDiscographyExample.hg19,
#         checkWithinMutantSeqs = TRUE
#     )
#
#     # Check correct nr. of proteotypic fragments.
#     testthat::expect_equal(
#         object = sum(ProteoDisco::mutantTranscripts(ProteoDiscographyExample.hg19)$genomicVariants$proteotypicFragmentsCount > 0, na.rm = TRUE),
#         expected = 20
#     )
#
# })