/usr/lib/R/site-library/SummarizedExperiment/unitTests/test_Assays-class.R is in r-bioc-summarizedexperiment 1.8.0-1.
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 | test_bind_Assays <- function() {
## unnamed -- map by position
l1 <- list(matrix(1, 3, 4), matrix(2, 3, 4))
l2 <- list(matrix(3, 3, 4), matrix(4, 3, 4))
a1 <- Assays(l1)
a2 <- Assays(l2)
target <- Map(rbind, l1, l2)
current <- rbind(a1, a2)
checkTrue(is(current, "ShallowSimpleListAssays"))
checkIdentical(as(target, "SimpleList"), as(current, "SimpleList"))
target <- Map(cbind, l1, l2)
current <- cbind(a1, a2)
checkTrue(is(current, "ShallowSimpleListAssays"))
checkIdentical(as(target, "SimpleList"), as(current, "SimpleList"))
## named -- map by name
l1 <- list(x=matrix(1, 3, 4), y=matrix(2, 3, 4))
l2 <- list(y=matrix(4, 3, 4), x=matrix(3, 3, 4))
a1 <- Assays(l1)
a2 <- Assays(l2)
target <- Map(rbind, l1, l2[match(names(l2), names(l1))])
current <- rbind(a1, a2)
checkTrue(is(current, "ShallowSimpleListAssays"))
checkIdentical(as(target, "SimpleList"), as(current, "SimpleList"))
target <- Map(cbind, l1, l2[match(names(l2), names(l1))])
current <- cbind(a1, a2)
checkTrue(is(current, "ShallowSimpleListAssays"))
checkIdentical(as(target, "SimpleList"), as(current, "SimpleList"))
}
test_bind_higher_order_Assays <- function() {
## unnamed -- map by position
l1 <- list(array(1, dim = c(3, 4, 5, 6)),
array(2, dim = c(3, 4, 5, 6)))
l2 <- list(array(4, dim = c(3, 4, 5, 6)),
array(3, dim = c(3, 4, 5, 6)))
a1 <- Assays(l1)
a2 <- Assays(l2)
target <- Map(arbind, l1, l2)
current <- rbind(a1, a2)
checkTrue(is(current, "ShallowSimpleListAssays"))
checkIdentical(as(target, "SimpleList"), as(current, "SimpleList"))
target <- Map(acbind, l1, l2)
current <- cbind(a1, a2)
checkTrue(is(current, "ShallowSimpleListAssays"))
checkIdentical(as(target, "SimpleList"), as(current, "SimpleList"))
## named -- map by name
l1 <- list(x = array(1, dim = c(3, 4, 5, 6)),
y = array(2, dim = c(3, 4, 5, 6)))
l2 <- list(y = array(4, dim = c(3, 4, 5, 6)),
x = array(3, dim = c(3, 4, 5, 6)))
a1 <- Assays(l1)
a2 <- Assays(l2)
target <- Map(arbind, l1, l2[match(names(l2), names(l1))])
current <- rbind(a1, a2)
checkTrue(is(current, "ShallowSimpleListAssays"))
checkIdentical(as(target, "SimpleList"), as(current, "SimpleList"))
target <- Map(acbind, l1, l2[match(names(l2), names(l1))])
current <- cbind(a1, a2)
checkTrue(is(current, "ShallowSimpleListAssays"))
checkIdentical(as(target, "SimpleList"), as(current, "SimpleList"))
}
test_bind_error_on_incompatible_dimension_Assays <- function() {
l1 <- list(x = array(1, dim = c(3, 4, 5, 6)),
y = array(2, dim = c(3, 4, 5, 6)))
l2 <- list(y = matrix(4, 3, 4), x = matrix(3, 3, 4))
a1 <- Assays(l1)
a2 <- Assays(l2)
## arbind
checkException(rbind(a1, a2), silent = TRUE)
checkException(arbind(l1[[1]], l2[[1]]), silent = TRUE)
## acbind
checkException(cbind(a1, a2), silent = TRUE)
checkException(acbind(l1[[1]], l2[[1]]), silent = TRUE)
}
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