/usr/lib/R/site-library/AnnotationDbi/unitTests/test_select_NOSCHEMA.R is in r-bioc-annotationdbi 1.26.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 | ## this will install a testDb stashed in the
## ## this is the package name
## pkgName <- "org.TguttataTestingSubset.eg.db"
## ## Get the package path
## pkgPath <- system.file("extdata", pkgName, package="AnnotationDbi")
## ## Then install it
## install.packages(pkgPath, repos=NULL)
## and load it
library("org.TguttataTestingSubset.eg.db")
x <- org.TguttataTestingSubset.eg.db
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")
## lower level tests (more useful)
test_keysLow <- function(){
res <- unique(AnnotationDbi:::.noSchemaKeys(x, "CHROMOSOME"))
checkTrue(all(sort(res) == sort(finchCsomes)))
}
test_selectLow <- function(){
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(){
res <- columns(x)
checkTrue(all(sort(res) == sort(finchCols)))
}
test_keytypes <- function(){
res <- keytypes(x)
checkTrue(all(sort(res) == sort(finchCols)))
}
test_keys<- function(){
## most basic case
res <- keys(x, "CHROMOSOME")
checkTrue(all(sort(res) == sort(finchCsomes)))
res <- head(keys(x, "GID"), n=2)
checkTrue(all(res==c("100008579","100008580")))
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(){
## 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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