/usr/lib/R/site-library/Biobase/UnitTests/AssayData_test.R is in r-bioc-biobase 2.14.0-1.
This file is owned by root:root, with mode 0o644.
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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 | checkAssayDataCombine <- function(nr, nc) {
obj1 <- assayDataNew(exprs=
matrix(runif(nr*nc), nrow=nr, ncol=nc,
dimnames=list(
if (nr > 0) letters[1:nr] else NULL,
if (nc > 0) LETTERS[1:nc] else NULL)))
obj <- combine(obj1,obj1)
checkTrue(!identical(obj, obj1)) # different environments
checkTrue(identical(obj1$exprs, obj$exprs))
storageMode(obj1) <- "list"
obj <- combine(obj1,obj1)
checkTrue(identical(obj1, obj)) # same list
checkTrue(identical(obj1$exprs, obj$exprs))
if (nc > 2) {
## combine distinct cols
obj1 <- assayDataNew(exprs=
matrix(runif(nr*nc), nrow=nr, ncol=nc,
dimnames=list(
if (nr > 0) letters[1:nr] else nr,
LETTERS[1:nc])))
obj2 <- obj1
sampleNames(obj2)[3] <- letters[3]
obj <- combine(obj1, obj2)
checkTrue(all(dim(obj$exprs)==c(nr,nc+1)))
checkTrue(identical(obj$exprs[,1:nc],obj1$exprs))
checkTrue(identical(obj$exprs[,nc+1], obj2$exprs[,3]))
}
if (nc > 1) {
## inconsistent data -- list, otherwise both copies change!
storageMode(obj1) <- "list"
obj2 <- obj1
obj2$exprs[,1] <- runif(nr)
checkException(combine(obj1, obj2), silent=TRUE)
}
}
testAssayDataCombine <- function() {
checkAssayDataCombine(5,3)
checkAssayDataCombine(0,0)
checkAssayDataCombine(1,0)
checkAssayDataCombine(0,1)
}
testAssayDataCombineRows <- function() {
m <- matrix(1:20, nrow=5,
dimnames=list(LETTERS[1:5], letters[1:4]))
obj <- assayDataNew(exprs=m)
obj1 <- assayDataNew(exprs=m[1:3,])
obj2 <- assayDataNew(exprs=m[4:5,])
checkEquals(obj, combine(obj1, obj2))
obj3 <- assayDataNew(exprs=m[3:5,])
checkEquals(obj, combine(obj1, obj3)) # overlapping
}
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