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## this will install a testDb stashed in the
## ## this is the package name
## pkgName <- "org.testing.db"
## ## Get the package path
## pkgPath <- system.file("extdata", pkgName, package="AnnotationDbi")
## ## Then install it
## install.packages(pkgPath, repos=NULL)
## and load it
#####install.packages(system.file('extdata','org.testing.db', package='AnnotationDbi'), repos=NULL)
dir.create(testlib <- tempfile())
old_libPaths <- NULL
.setUp <- function()
{
installed <- rownames(installed.packages(testlib))
if ("org.testing.db" %in% installed)
return()
pkg <- system.file("extdata", "org.testing.db", package="AnnotationDbi")
suppressPackageStartupMessages(install.packages(
pkg, lib = testlib, repos=NULL, type="source",
INSTALL_opts="--no-test-load", verbose = FALSE, quiet = TRUE
))
old_libPaths <<- .libPaths()
.libPaths(c(testlib, old_libPaths))
finchCsomes <<- c(as.character(1:15),as.character(17:28),
"MT","Un","W","Z","4A","1A","1B")
finchCols <<- c("CHROMOSOME","SYMBOL","GENENAME","GID","GO","EVIDENCE",
"ONTOLOGY","GOALL","EVIDENCEALL","ONTOLOGYALL")
}
.tearDown <- function()
.libPaths(old_libPaths)
## lower level tests (more useful)
test_keysLow <- function(){
x <- org.testing.db::org.testing.db
res <- unique(AnnotationDbi:::.noSchemaKeys(x, "CHROMOSOME"))
checkTrue(all(sort(res) == sort(finchCsomes)))
}
test_selectLow <- function(){
x <- org.testing.db::org.testing.db
keys <- "100008579"
cols <- "SYMBOL"
keytype <- "GID"
res <- AnnotationDbi:::.noSchemaSelect(x, keys, cols, keytype)
checkTrue(all(res==c("100008579","EGR1")))
checkTrue(all(colnames(res)==c("GID","SYMBOL")))
keys <- "brain-derived neurotrophic factor"
cols <- c("SYMBOL","GID")
keytype <- "GENENAME"
res <- AnnotationDbi:::.noSchemaSelect(x, keys, cols, keytype)
checkTrue(all(res==c("brain-derived neurotrophic factor","BDNF","751584")))
checkTrue(all(colnames(res)==c("GENENAME","SYMBOL","GID")))
keys <- "brain-derived neurotrophic factor"
cols <- c("GO","GID")
keytype <- "GENENAME"
res <- head(AnnotationDbi:::.noSchemaSelect(x, keys, cols, keytype),n=1)
checkTrue(all(res==c("brain-derived neurotrophic factor","GO:0001657",
"751584")))
checkTrue(all(colnames(res)==c("GENENAME","GO","GID")))
}
## high level tests (does this dispatch right etc.?)
test_columns <- function(){
x <- org.testing.db::org.testing.db
res <- columns(x)
checkTrue(all(sort(res) == sort(finchCols)))
}
test_keytypes <- function(){
x <- org.testing.db::org.testing.db
res <- keytypes(x)
checkTrue(all(sort(res) == sort(finchCols)))
}
test_keys<- function(){ ## BOOM
x <- org.testing.db::org.testing.db
## most basic case
res <- keys(x, "CHROMOSOME")
checkTrue(all(sort(res) == sort(finchCsomes)))
res <- head(keys(x, "GID"), n=2)
checkTrue(all(res==c("751582", "751583")))
res <- head(keys(x, "SYMBOL", pattern="BDNF"))
checkTrue(res=="BDNF")
res <- head(keys(x, "GID", pattern="BDNF", column="SYMBOL"))
checkTrue(res=="751584")
res <- head(keys(x, "SYMBOL", column="GID"),n=2)
checkTrue(all(res==c("ACT5C","AHSA2")))
}
test_select <- function(){
x <- org.testing.db::org.testing.db
## most basic case
res <- select(x, keys="100008579",
columns="SYMBOL", keytype="GID")
checkTrue(all(res==c("100008579","EGR1")))
checkTrue(all(colnames(res)==c("GID","SYMBOL")))
## return more than one column
res <- select(x, keys="100008579",
columns=c("SYMBOL","CHROMOSOME"), keytype="GID")
checkTrue(all(res==c("100008579","EGR1","13")))
checkTrue(all(colnames(res)==c("GID","SYMBOL","CHROMOSOME")))
## return GO and evidence codes
suppressWarnings(res <- head(select(x, keys="100008579",
columns=c("GO","EVIDENCE"), keytype="GID"),n=1))
checkTrue(all(res==c("100008579","GO:0000122","IEA")))
checkTrue(all(colnames(res)==c("GID","GO","EVIDENCE")))
## test lookup from alt-key
res <- select(x, keys="BDNF",
columns="GENENAME", keytype="SYMBOL")
checkTrue(all(res==c("BDNF","brain-derived neurotrophic factor")))
checkTrue(all(colnames(res)==c("SYMBOL","GENENAME")))
}
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