context("create_ensembl_query_func")
test_that("create_ensembl_query_func works", {
# get all records
ensembl <- readRDS(system.file("extdata", "ensembl_small.rds", package="qtl2bioc"))
qf <- create_ensembl_query_func(ensembl, FALSE)
expected <- structure(list(chr = c("2", "2", "2", "2", "2", "2", "2", "2", "2"),
start = c(96.318169, 96.318169, 96.318216, 96.987018, 96.987018,
96.987018, 96.999624, 96.999624, 96.999624),
stop = c(97.631666, 97.631666, 97.630983, 97.083561, 97.083561,
96.987138, 97.000293, 97.000293, 97.000293),
width = c(1313498L, 1313498L, 1312768L, 96544L, 96544L, 121L, 670L, 670L, 670L),
strand = c("+", "+", "+", "-", "-", "-", "+", "+", "+"),
source = c("ensembl_havana", "havana", "havana", "havana", "havana", "havana", "havana", "havana", "havana"),
type = c("gene", "transcript", "transcript", "gene", "transcript", "exon", "gene", "transcript", "exon"),
score = c(NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_),
phase = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_),
gene_id = c("ENSMUSG00000050587", "ENSMUSG00000050587", "ENSMUSG00000050587",
"ENSMUSG00000091061", "ENSMUSG00000091061", "ENSMUSG00000091061",
"ENSMUSG00000091288", "ENSMUSG00000091288", "ENSMUSG00000091288"),
gene_version = c("14", "14", "14", "1", "1", "1", "1", "1", "1"),
Name = c("Lrrc4c", "Lrrc4c", "Lrrc4c", "4930445B16Rik", "4930445B16Rik", "4930445B16Rik", "Gm17075", "Gm17075", "Gm17075"),
gene_source = c("ensembl_havana", "ensembl_havana", "ensembl_havana", "havana", "havana", "havana", "havana", "havana", "havana"),
gene_biotype = c("protein_coding", "protein_coding", "protein_coding", "lincRNA", "lincRNA", "lincRNA", "processed_pseudogene",
"processed_pseudogene", "processed_pseudogene"),
havana_gene = c("OTTMUSG00000014522", "OTTMUSG00000014522", "OTTMUSG00000014522", "OTTMUSG00000036475",
"OTTMUSG00000036475", "OTTMUSG00000036475", "OTTMUSG00000036477",
"OTTMUSG00000036477", "OTTMUSG00000036477"),
havana_gene_version = c("6", "6", "6", "1", "1", "1", "1", "1", "1"),
transcript_id = c(NA, "ENSMUST00000135431", "ENSMUST00000162807", NA, "ENSMUST00000170085",
"ENSMUST00000170085", NA, "ENSMUST00000171924", "ENSMUST00000171924"),
transcript_version = c(NA, "7", "8", NA, "1", "1", NA, "1", "1"),
transcript_name = c(NA, "Lrrc4c-001", "Lrrc4c-002", NA, "4930445B16Rik-001", "4930445B16Rik-001",
NA, "Gm17075-001", "Gm17075-001"),
transcript_source = c(NA, "havana", "havana", NA, "havana", "havana", NA, "havana", "havana"),
transcript_biotype = c(NA, "protein_coding", "protein_coding", NA, "lincRNA", "lincRNA",
NA, "processed_pseudogene", "processed_pseudogene"),
havana_transcript = c(NA, "OTTMUST00000034453", "OTTMUST00000093478", NA, "OTTMUST00000093476",
"OTTMUST00000093476", NA, "OTTMUST00000093481", "OTTMUST00000093481"),
havana_transcript_version = c(NA, "3", "1", NA, "1", "1", NA, "1", "1"),
tag = c(NA, "basic", "basic", NA, "basic", "basic", NA, "basic", "basic"),
transcript_support_level = c(NA, "1", "1", NA, "1", "1", NA, "NA", "NA"),
exon_number = c(NA, NA, NA, NA, NA, "5", NA, NA, "1"),
exon_id = c(NA, NA, NA, NA, NA, "ENSMUSE00000882453", NA, NA, "ENSMUSE00000877806"),
exon_version = c(NA, NA, NA, NA, NA, "1", NA, NA, "1"),
ccds_id = c(NA, "CCDS16460", "CCDS16460", NA, NA, NA, NA, NA, NA),
protein_id = c(NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_),
protein_version = c(NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_)),
.Names = c("chr", "start", "stop", "width", "strand", "source", "type", "score", "phase", "gene_id", "gene_version",
"Name", "gene_source", "gene_biotype", "havana_gene", "havana_gene_version", "transcript_id",
"transcript_version", "transcript_name", "transcript_source", "transcript_biotype", "havana_transcript",
"havana_transcript_version", "tag", "transcript_support_level", "exon_number", "exon_id", "exon_version",
"ccds_id", "protein_id", "protein_version"),
row.names = c(NA,-9L), class = "data.frame")
expect_equal(qf(2, 96.9, 97.0), expected)
# only full genes
qf2 <- create_ensembl_query_func(ensembl, TRUE)
expected_sub <- expected[c(1,4,7),,drop=FALSE]
expect_equal(qf2(2, 96.9, 97), expected_sub)
})
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