Nothing
context("create_variant_query_func")
test_that("create_variant_query_func works", {
# use file name
dbfile <- system.file("extdata", "cc_variants_small.sqlite", package="qtl2")
qf <- create_variant_query_func(dbfile)
expected <- structure(list(snp = c("rs213863525", "rs235573572", "rs253240367"),
chr = c("2", "2", "2"), pos = c(97.300098, 97.30014, 97.300197),
alleles = c("A|T", "T|C", "G|T"), sdp = c(32L, 64L, 64L),
ensembl_gene = rep("ENSMUSG00000050587", 3),
consequence = rep("ENSMUSG00000050587:intron_variant", 3),
A_J = c(1L, 1L, 1L),
C57BL_6J = c(1L, 1L, 1L),
"129S1_SvImJ" = c(1L, 1L, 1L),
NOD_ShiLtJ = c(1L, 1L, 1L),
NZO_HlLtJ = c(1L, 1L, 1L),
CAST_EiJ = c(2L, 1L, 1L),
PWK_PhJ = c(1L, 2L, 2L),
WSB_EiJ = c(1L, 1L, 1L),
type = c("snp", "snp", "snp")),
.Names = c("snp", "chr", "pos", "alleles", "sdp", "ensembl_gene", "consequence",
"A_J", "C57BL_6J", "129S1_SvImJ", "NOD_ShiLtJ", "NZO_HlLtJ", "CAST_EiJ", "PWK_PhJ", "WSB_EiJ",
"type"),
row.names = c(NA, -3L), class = "data.frame")
expect_equal(qf(2, 97.3, 97.3002), expected)
# use db connection
library(RSQLite)
db <- dbConnect(SQLite(), dbfile)
qf2 <- create_variant_query_func(db=db)
expect_equal(qf2(2, 97.3, 97.3002), expected)
dbDisconnect(db)
# include filter
qf3 <- create_variant_query_func(dbfile, filter="snp_id = 'rs235573572'")
expected_sub <- expected[2,,drop=FALSE]
rownames(expected_sub) <- 1L
expect_equal(qf3(2, 0, 200), expected_sub)
})
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