Nothing
context("create_gene_query_func")
test_that("create_gene_query_func works", {
# use file name
dbfile <- system.file("extdata", "mouse_genes_small.sqlite", package="qtl2")
qf <- create_gene_query_func(dbfile)
expected <- structure(list(chr = c("2", "2", "2"),
source = c("MGI", "MGI", "MGI"),
type = c("gene", "gene", "pseudogene"),
start = c(96.318169, 97.626967, 97.947953),
stop = c(97.631672, 97.627052, 97.949756),
score = c(NA_real_, NA_real_, NA_real_),
strand = c("+", "-", "-"),
phase = c(NA_real_, NA_real_, NA_real_),
ID = c("MGI_C57BL6J_2442636", "MGI_C57BL6J_5690712", "MGI_C57BL6J_3651056"),
Name = c("Lrrc4c", "Gm44320", "Gm13803"),
Parent = c(NA_character_, NA_character_, NA_character_),
Dbxref = c("NCBI_Gene:241568,ENSEMBL:ENSMUSG00000050587",
"ENSEMBL:ENSMUSG00000105133",
"NCBI_Gene:621146,ENSEMBL:ENSMUSG00000082820"),
gene_id = c("MGI:2442636", "MGI:5690712", "MGI:3651056"),
mgi_type = c("protein coding gene", "miRNA gene", "pseudogene"),
description=c("leucine rich repeat containing 4C",
"predicted gene%2c 44320",
"predicted gene 13803")),
.Names = c("chr", "source", "type", "start", "stop", "score", "strand",
"phase", "ID", "Name", "Parent", "Dbxref", "gene_id", "mgi_type", "description"),
row.names = c(NA, -3L), class = "data.frame")
expect_equal(qf(2, 97.5, 98.0), expected)
# use db connection
library(RSQLite)
db <- dbConnect(SQLite(), dbfile)
qf2 <- create_gene_query_func(db=db)
expect_equal(qf2(2, 97.5, 98.0), expected)
dbDisconnect(db)
# include filter
qf3 <- create_gene_query_func(dbfile, filter="Name = 'Lrrc4c'")
expected_sub <- expected[1,,drop=FALSE]
rownames(expected_sub) <- 1L
expect_equal(qf3(2, 97.5, 98), expected_sub)
})
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.