Nothing
context("searchVariantsByGeneSymbol")
library(org.Hs.eg.db)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
test_that("searchVariantsByGeneSymbol works", {
skip_on_bioc()
host <- "http://1kgenomes.ga4gh.org/"
datasetId <- searchDatasets(host, nrows = 1)$id
variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id
variants <- searchVariantsByGeneSymbol(host = host,
variantSetId = variantSetId,seqlevelsStyle = "NCBI",
geneSymbol = "SCN1A", orgDb = "org.Hs.eg.db",
txDb = "TxDb.Hsapiens.UCSC.hg19.knownGene")
expect_s4_class(variants, "DataFrame")
expect_equal(dim(variants), c(4227, 33))
})
test_that("searchVariantsByGeneSymbol feature=transcripts works", {
skip_on_bioc()
host <- "http://1kgenomes.ga4gh.org/"
datasetId <- searchDatasets(host, nrows = 1)$id
variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id
variants <- searchVariantsByGeneSymbol(host = host,
variantSetId = variantSetId,seqlevelsStyle = "NCBI",
geneSymbol = "SCN1A", orgDb = "org.Hs.eg.db",
txDb = "TxDb.Hsapiens.UCSC.hg19.knownGene", feature = transcripts)
expect_s4_class(variants, "DataFrame")
expect_equal(dim(variants), c(8547, 33))
})
test_that("searchVariantsByGeneSymbol feature=exons works", {
skip_on_bioc()
host <- "http://1kgenomes.ga4gh.org/"
datasetId <- searchDatasets(host, nrows = 1)$id
variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id
variants <- searchVariantsByGeneSymbol(host = host,
variantSetId = variantSetId, seqlevelsStyle = "NCBI",
geneSymbol = "A1BG", orgDb = "org.Hs.eg.db",
txDb = "TxDb.Hsapiens.UCSC.hg19.knownGene", feature = exons)
expect_s4_class(variants, "DataFrame")
expect_equal(dim(variants), c(140, 24))
})
test_that("searchVariantsByGeneSymbol feature=cds works", {
skip_on_bioc()
host <- "http://1kgenomes.ga4gh.org/"
datasetId <- searchDatasets(host, nrows = 1)$id
variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id
variants <- searchVariantsByGeneSymbol(host = host,
variantSetId = variantSetId,seqlevelsStyle = "NCBI", geneSymbol = "SCN1A",
"org.Hs.eg.db", "TxDb.Hsapiens.UCSC.hg19.knownGene", feature = cds)
expect_s4_class(variants, "DataFrame")
expect_equal(dim(variants), c(124, 24))
})
test_that("searchVariantsByGeneSymbol feature=promoters works", {
skip_on_bioc()
host <- "http://1kgenomes.ga4gh.org/"
datasetId <- searchDatasets(host, nrows = 1)$id
variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id
variants <- searchVariantsByGeneSymbol(host = host,
variantSetId = variantSetId,seqlevelsStyle = "NCBI", geneSymbol = "SCN1A",
"org.Hs.eg.db", "TxDb.Hsapiens.UCSC.hg19.knownGene", feature = promoters)
expect_s4_class(variants, "DataFrame")
expect_equal(dim(variants), c(177, 24))
})
test_that("searchVariantsByGeneSymbol multiple genes works", {
skip_on_bioc()
host <- "http://1kgenomes.ga4gh.org/"
datasetId <- searchDatasets(host, nrows = 1)$id
variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id
variants <- searchVariantsByGeneSymbol(host = host,
variantSetId = variantSetId,seqlevelsStyle = "NCBI",
geneSymbol = c("A1BG", "SCN1A"), orgDb = "org.Hs.eg.db",
txDb = "TxDb.Hsapiens.UCSC.hg19.knownGene")
expect_s4_class(variants, "DataFrame")
expect_equal(dim(variants), c(4770, 34))
})
test_that("searchVariantsByGeneSymbol multiple genes feature=transcripts works", {
skip_on_bioc()
host <- "http://1kgenomes.ga4gh.org/"
datasetId <- searchDatasets(host, nrows = 1)$id
variantSetId <- searchVariantSets(host, datasetId, nrows = 1)$id
variants <- searchVariantsByGeneSymbol(host = host,
variantSetId = variantSetId,seqlevelsStyle = "NCBI",
geneSymbol = c("A1BG", "SCN1A"), orgDb = "org.Hs.eg.db",
txDb = "TxDb.Hsapiens.UCSC.hg19.knownGene", feature = transcripts)
expect_s4_class(variants, "DataFrame")
expect_equal(dim(variants), c(9263, 34))
})
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