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## unit test to just check that mapIds is behaving itself
require(org.Hs.eg.db)
## constants
k <- head(keys(org.Hs.eg.db, 'ENTREZID'))
# trace("mapIds", tracer=browser, signature ="AnnotationDb")
### The actual tests.
## Default is currently 'first'
test_mapIds_default <- function(){
res <- mapIds(org.Hs.eg.db, keys=k, column='ALIAS', keytype='ENTREZID')
checkTrue(length(res) == length(k))
checkTrue(res[[1]] == "A1B")
checkTrue(class(res)=='character')
}
## test other return types.
## "list"
test_mapIds_CharacterList <- function(){
res <- mapIds(org.Hs.eg.db, keys=k, column='ALIAS', keytype='ENTREZID',
multiVals="list")
checkTrue(length(res) == length(k))
checkTrue(res[[1]][1] == "A1B")
checkTrue(class(res)=='list')
}
## "CharacterList"
test_mapIds_CharacterList <- function(){
res <- mapIds(org.Hs.eg.db, keys=k, column='ALIAS', keytype='ENTREZID',
multiVals="CharacterList")
checkTrue(length(res) == length(k))
checkTrue(res[[1]][1] == "A1B")
checkTrue(class(res)=='SimpleCharacterList')
}
## "NAMultiples"
test_mapIds_NAMultiples <- function(){
res <- mapIds(org.Hs.eg.db, keys=k, column='PFAM', keytype='ENTREZID',
multiVals="asNA")
checkTrue(length(res) == length(k))
checkTrue(res[['10']] == "PF00797")
checkTrue(class(res)=='character')
res <- mapIds(org.Hs.eg.db, "2", "PFAM", "ENTREZID", multiVals = "asNA")
checkTrue(is.character(res))
checkIdentical(length(res), 1L)
}
## "filterMultiples"
test_mapIds_filterMultiples <- function(){
res <- mapIds(org.Hs.eg.db, keys=k, column='PFAM', keytype='ENTREZID',
multiVals="filter")
checkTrue(length(res) < length(k)) ## multi matchers means should be shorter
checkTrue(res[['10']] == "PF00797")
checkTrue(res[['1']] == "PF13895")
checkTrue(class(res)=='character')
res <- mapIds(org.Hs.eg.db, "2", "PFAM", "ENTREZID", multiVals = "filter")
checkTrue(is.character(res))
checkIdentical(length(res), 0L)
}
## CUSTOM function
test_mapIds_FUN <- function(){
last <- function(x){
x[[length(x)]]
}
res <- mapIds(org.Hs.eg.db, keys=k, column='ALIAS', keytype='ENTREZID',
multiVals=last)
checkTrue(length(res) == length(k))
checkTrue(res[[1]] == "A1BG")
checkTrue(class(res)=='character')
}
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