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#setAutoRealizationBackend("RleArray")
#setAutoRealizationBackend("HDF5Array")
test_DelayedArray_constructor <- function()
{
check_DelayedMatrix <- function(m, M) {
checkTrue(is(M, "DelayedMatrix"))
checkTrue(validObject(M, complete=TRUE))
checkIdentical(typeof(m), type(M))
checkIdentical(typeof(m), type(M[ , -2]))
checkIdentical(typeof(m), type(M[ , 0]))
checkIdentical(typeof(m), type(M[0 , ]))
checkIdentical(dim(m), dim(M))
checkIdentical(rownames(m), rownames(M))
checkIdentical(colnames(m), colnames(M))
}
## 6-col seed
DF1 <- DataFrame(aa=1:5,
bb=letters[1:5],
cc=Rle(c(-0.25, 7.1), 3:2),
dd=factor(c("E", "B", "A", "A", "B"), levels=LETTERS),
ee=Rle(factor(c("d", "b"), levels=letters[1:5]), 2:3),
ff=c(FALSE, TRUE, TRUE, FALSE, FALSE))
df1 <- as.data.frame(DF1)
m1 <- as.matrix(df1) # character matrix
M1a <- DelayedArray(m1) # matrix seed
check_DelayedMatrix(m1, M1a)
checkIdentical(m1, as.matrix(M1a))
checkIdentical(m1, as.array(M1a))
M1b <- DelayedArray(df1) # data.frame seed
rownames(M1b) <- NULL
check_DelayedMatrix(m1, M1b)
M1c <- DelayedArray(DF1) # DataFrame seed
check_DelayedMatrix(m1, M1c)
## 5-col seed
DF2 <- DF1[ , -2, drop=FALSE]
df2 <- as.data.frame(DF2)
m2 <- as.matrix(df2) # character matrix
M2a <- DelayedArray(m2) # matrix seed
check_DelayedMatrix(m2, M2a)
checkIdentical(m2, as.matrix(M2a))
checkIdentical(m2, as.array(M2a))
M2b <- DelayedArray(df2) # data.frame seed
rownames(M2b) <- NULL
check_DelayedMatrix(m2, M2b)
M2c <- DelayedArray(DF2) # DataFrame seed
check_DelayedMatrix(m2, M2c)
## 4-col seed
DF3 <- DF1[ , -c(2, 4), drop=FALSE]
df3 <- as.data.frame(DF3)
m3 <- as.matrix(df3) # character matrix
M3a <- DelayedArray(m3) # matrix seed
check_DelayedMatrix(m3, M3a)
checkIdentical(m3, as.matrix(M3a))
checkIdentical(m3, as.array(M3a))
M3b <- DelayedArray(df3) # data.frame seed
rownames(M3b) <- NULL
check_DelayedMatrix(m3, M3b)
M3c <- DelayedArray(DF3) # DataFrame seed
check_DelayedMatrix(m3, M3c)
## 3-col seed
DF4 <- DF1[ , -c(2, 4, 5), drop=FALSE]
df4 <- as.data.frame(DF4)
m4 <- as.matrix(df4) # double matrix
M4a <- DelayedArray(m4) # matrix seed
check_DelayedMatrix(m4, M4a)
checkIdentical(m4, as.matrix(M4a))
checkIdentical(m4, as.array(M4a))
M4b <- DelayedArray(df4) # data.frame seed
rownames(M4b) <- NULL
check_DelayedMatrix(m4, M4b)
checkIdentical(m4, as.matrix(M4b))
checkIdentical(m4, as.array(M4b))
M4c <- DelayedArray(DF4) # DataFrame seed
check_DelayedMatrix(m4, M4c)
checkIdentical(m4, as.matrix(M4c))
checkIdentical(m4, as.array(M4c))
## 2-col seed
DF5 <- DF1[ , c(1, 6), drop=FALSE]
df5 <- as.data.frame(DF5)
m5 <- as.matrix(df5) # integer matrix
M5a <- DelayedArray(m5) # matrix seed
check_DelayedMatrix(m5, M5a)
checkIdentical(m5, as.matrix(M5a))
checkIdentical(m5, as.array(M5a))
M5b <- DelayedArray(df5) # data.frame seed
rownames(M5b) <- NULL
check_DelayedMatrix(m5, M5b)
checkIdentical(m5, as.matrix(M5b))
checkIdentical(m5, as.array(M5b))
M5c <- DelayedArray(DF5) # DataFrame seed
check_DelayedMatrix(m5, M5c)
checkIdentical(m5, as.matrix(M5c))
checkIdentical(m5, as.array(M5c))
## 1-col seed
DF6 <- DF1[ , 6, drop=FALSE]
df6 <- as.data.frame(DF6)
m6 <- as.matrix(df6) # logical matrix
M6a <- DelayedArray(m6) # matrix seed
check_DelayedMatrix(m6, M6a)
checkIdentical(m6, as.matrix(M6a))
checkIdentical(m6, as.array(M6a))
M6b <- DelayedArray(df6) # data.frame seed
rownames(M6b) <- NULL
check_DelayedMatrix(m6, M6b)
checkIdentical(m6, as.matrix(M6b))
checkIdentical(m6, as.array(M6b))
M6c <- DelayedArray(DF6) # DataFrame seed
check_DelayedMatrix(m6, M6c)
checkIdentical(m6, as.matrix(M6c))
checkIdentical(m6, as.array(M6c))
}
test_DelayedArray_subsetting <- function()
{
a <- array(runif(78000), dim=c(600, 26, 5),
dimnames=list(NULL, LETTERS, letters[1:5]))
A <- realize(a)
checkTrue(is(A, "DelayedArray"))
checkTrue(validObject(A, complete=TRUE))
checkIdentical(a, as.array(A[ , , ]))
checkException(A[ , 27, ], silent=TRUE)
checkException(A[ , , "f"], silent=TRUE)
target <- a[0, , ]
checkIdentical(target, as.array(A[0, , ]))
checkIdentical(target, as.array(A[integer(0), , ]))
checkIdentical(target, as.array(A[NULL, , ]))
target <- a[ , 0, ]
checkIdentical(target, as.array(A[ , 0, ]))
checkIdentical(target, as.array(A[ , integer(0), ]))
checkIdentical(target, as.array(A[ , NULL, ]))
target <- a[ , , 0]
checkIdentical(target, as.array(A[ , , 0]))
checkIdentical(target, as.array(A[ , , integer(0)]))
checkIdentical(target, as.array(A[ , , NULL]))
target <- a[ , 0, 0]
checkIdentical(target, as.array(A[ , 0, 0]))
checkIdentical(target, as.array(A[ , integer(0), integer(0)]))
checkIdentical(target, as.array(A[ , NULL, NULL]))
target <- a[0, , 0]
checkIdentical(target, as.array(A[0, , 0]))
checkIdentical(target, as.array(A[integer(0), , integer(0)]))
checkIdentical(target, as.array(A[NULL, , NULL]))
target <- a[0, 0, ]
checkIdentical(target, as.array(A[0, 0, ]))
checkIdentical(target, as.array(A[integer(0), integer(0), ]))
checkIdentical(target, as.array(A[NULL, NULL, ]))
target <- a[0, 0, 0]
checkIdentical(target, as.array(A[0, 0, 0]))
checkIdentical(target, as.array(A[integer(0), integer(0), integer(0)]))
checkIdentical(target, as.array(A[NULL, NULL, NULL]))
i <- c(FALSE, TRUE)
target <- a[i, , ]
checkIdentical(target, as.array(A[i, , ]))
target <- a[i, 0, ]
checkIdentical(target, as.array(A[i, 0, ]))
checkIdentical(target, as.array(A[i, integer(0), ]))
checkIdentical(target, as.array(A[i, NULL, ]))
i <- c(FALSE, TRUE, TRUE, FALSE, FALSE)
target <- a[i, , ]
checkIdentical(target, as.array(A[i, , ]))
target <- a[i, 0, ]
checkIdentical(target, as.array(A[i, 0, ]))
checkIdentical(target, as.array(A[i, integer(0), ]))
checkIdentical(target, as.array(A[i, NULL, ]))
k <- c(TRUE, FALSE)
target <- a[ , , k]
checkIdentical(target, as.array(A[ , , k]))
target <- a[0, , k]
checkIdentical(target, as.array(A[0, , k]))
checkIdentical(target, as.array(A[integer(0), , k]))
checkIdentical(target, as.array(A[NULL, , k]))
target <- a[i, , k]
checkIdentical(target, as.array(A[i, , k]))
target <- a[i, 0, k]
checkIdentical(target, as.array(A[i, 0, k]))
checkIdentical(target, as.array(A[i, integer(0), k]))
checkIdentical(target, as.array(A[i, NULL, k]))
j <- c(20:5, 11:22)
target <- a[0, j, ]
checkIdentical(target, as.array(A[0, j, ]))
checkIdentical(target, as.array(A[integer(0), j, ]))
checkIdentical(target, as.array(A[NULL, j, ]))
target <- a[0, j, 0]
checkIdentical(target, as.array(A[0, j, 0]))
checkIdentical(target, as.array(A[integer(0), j, integer(0)]))
checkIdentical(target, as.array(A[NULL, j, NULL]))
target <- a[99:9, j, ]
checkIdentical(target, as.array(A[99:9, j, ]))
k <- c("e", "b", "b", "d", "e", "c")
target <- a[-3, j, k]
checkIdentical(target, as.array(A[-3, j, k]))
target <- a[-3, -j, k]
checkIdentical(target, as.array(A[-3, -j, k]))
target <- a[-3, -j, ]
checkIdentical(target, as.array(A[-3, -j, ]))
target <- a[-3, -j, -555555]
checkIdentical(target, as.array(A[-3, -j, -555555]))
target <- a[99:9, j, k]
checkIdentical(target, as.array(A[99:9, j, k]))
i <- c(150:111, 88:90, 75:90)
target <- a[i, j, k]
checkIdentical(target, as.array(A[i, j, k]))
target1 <- a[99, j, k]
checkIdentical(target1, as.matrix(A[99, j, k]))
B1 <- A[99, j, k]
checkIdentical(target1, as.array(B1))
target <- target1[15:8, c("c", "b")]
checkIdentical(target, as.array(B1[15:8, c("c", "b")]))
target <- target1[0, ]
checkIdentical(target, as.array(B1[0, ]))
target <- target1[ , 0]
checkIdentical(target, as.array(B1[ , 0]))
target <- target1[0, 0]
checkIdentical(target, as.array(B1[0, 0]))
target2 <- a[i, 22, k]
checkIdentical(target2, as.matrix(A[i, 22, k]))
B2 <- A[i, 22, k]
checkIdentical(target2, as.array(B2))
target <- target2[15:8, c("c", "b")]
checkIdentical(target, as.array(B2[15:8, c("c", "b")]))
target <- target2[0, ]
checkIdentical(target, as.array(B2[0, ]))
target <- target2[ , 0]
checkIdentical(target, as.array(B2[ , 0]))
target <- target2[0, 0]
checkIdentical(target, as.array(B2[0, 0]))
target3 <- a[i, j, 5]
checkIdentical(target3, as.matrix(A[i, j, 5]))
B3 <- A[i, j, 5]
checkIdentical(target3, as.array(B3))
target <- target3[15:8, LETTERS[18:12]]
checkIdentical(target, as.array(B3[15:8, LETTERS[18:12]]))
target <- target3[0, ]
checkIdentical(target, as.array(B3[0, ]))
target <- target3[ , 0]
checkIdentical(target, as.array(B3[ , 0]))
target <- target3[0, 0]
checkIdentical(target, as.array(B3[0, 0]))
}
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