/usr/lib/R/site-library/S4Vectors/unitTests/test_FilterRules.R is in r-bioc-s4vectors 0.16.0-1.
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 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 | test_FilterRules_construct <- function() {
## as a simple character vector
filts <- c("peaks", "promoters")
parsedFilts <- list(peaks = expression(peaks),
promoters = expression(promoters))
filters <- FilterRules()
checkTrue(validObject(filters))
checkIdentical(as.list(filters), list())
filters <- FilterRules(filts)
checkTrue(validObject(filters))
checkIdentical(as.list(filters), parsedFilts)
checkIdentical(active(filters), structure(rep(TRUE, 2), names=filts))
## with functions and expressions
filts <- c(parsedFilts, list(find_eboxes = function(rd) rep(FALSE, nrow(rd))))
filters <- FilterRules(filts, active = FALSE)
checkTrue(validObject(filters))
filts$find_eboxes <- new("FilterClosure", filts$find_eboxes)
checkIdentical(as.list(filters), filts)
checkIdentical(active(filters), structure(rep(FALSE, 3), names=names(filts)))
## direct, quoted args (character literal parsed)
filters <- FilterRules(under_peaks = peaks, in_promoters = "promoters")
filts <- list(under_peaks = expression(peaks),
in_promoters = expression(promoters))
checkTrue(validObject(filters))
checkIdentical(as.list(filters), filts)
## mix them up
filters <- FilterRules(filts, diffexp = de)
checkTrue(validObject(filters))
checkIdentical(as.list(filters), c(filts, list(diffexp = expression(de))))
filts <- as.list(filters)
checkException(FilterRules(c(filts, 1)), silent = TRUE)
checkException(FilterRules(filts, active = filts), silent = TRUE)
checkException(FilterRules(list(find_eboxes = function() NULL)),
silent = TRUE)
}
test_FilterRules_append <- function() {
filts <- c("peaks", "promoters")
filts2 <- c("introns", "exons")
filters <- FilterRules(filts)
filters2 <- FilterRules(filts2, active=FALSE)
both <- append(filters, filters2)
checkTrue(validObject(both))
bothFilts <- structure(list(quote(peaks), quote(promoters),
quote(introns), quote(exons)),
names = c(filts, filts2))
checkIdentical(unlist(as.list(both)), bothFilts)
bothActive <- structure(c(TRUE, TRUE, FALSE, FALSE), names = names(bothFilts))
checkIdentical(active(both), bothActive)
both <- c(filters, filters2)
checkTrue(validObject(both))
checkIdentical(unlist(as.list(both)), bothFilts)
checkIdentical(active(both), bothActive)
filters[["cons"]] <- "cons"
filts <- list(peaks = quote(peaks), promoters = quote(promoters))
filts <- c(filts, cons = quote(cons))
checkIdentical(unlist(as.list(filters)), filts)
filters[["cons"]] <- quote(cons)
checkIdentical(unlist(as.list(filters)), filts)
filters[["cons"]] <- expression(cons)
checkIdentical(unlist(as.list(filters)), filts)
fun <- function(rd) rep(FALSE, nrow(rd))
filters[[4]] <- fun
filts <- c(filts, X = new("FilterClosure", fun))
checkIdentical(unlist(as.list(filters)), filts)
checkException(filters[[]] <- "threeprime", silent = TRUE)
checkException(filters[[1]] <- 2, silent = TRUE)
checkException(filters[[1]] <- list(quote(foo), quote(bar)), silent = TRUE)
}
test_FilterRules_subset <- function() {
filts <- c("peaks", "promoters", "introns")
filters <- FilterRules(filts)
checkIdentical(sapply(unlist(filters[1:2]), deparse),
structure(filts[1:2], names = filts[1:2]))
checkIdentical(sapply(unlist(filters[]),deparse),
structure(filts, names = filts))
checkException(filters[1,2], silent = TRUE)
}
test_FilterRules_active <- function() {
filts <- c("peaks", "promoters", "introns")
filters <- FilterRules(filts)
## set the active state directly
active(filters) <- FALSE
checkIdentical(active(filters), structure(rep(FALSE, 3), names = filts))
active(filters) <- TRUE
checkIdentical(active(filters), structure(rep(TRUE, 3), names = filts))
active(filters) <- c(FALSE, FALSE, TRUE)
checkIdentical(active(filters),
structure(c(FALSE, FALSE, TRUE), names = filts))
active(filters)["promoters"] <- TRUE
checkIdentical(active(filters),
structure(c(FALSE, TRUE, TRUE), names = filts))
checkException(active(filters) <- rep(FALSE, 2), silent = TRUE)
checkException(active(filters) <- rep(FALSE, 5), silent = TRUE)
checkException(active(filters)["introns"] <- NA, silent = TRUE)
## toggle the active state by name or index
active(filters) <- c(NA, 2) # NA's are dropped
checkIdentical(active(filters),
structure(c(FALSE, TRUE, FALSE), names = filts))
active(filters) <- c("peaks", NA)
checkIdentical(active(filters),
structure(c(TRUE, FALSE, FALSE), names = filts))
checkException(active(filters) <- "foo", silent = TRUE)
checkException(active(filters) <- 15, silent = TRUE)
}
test_FilterRules_annotation <- function() {
filts <- c("peaks", "promoters")
filters <- FilterRules(filts)
mcols(filters) <- DataFrame(a = 1:2)
checkIdentical(mcols(filters)[,1], 1:2)
checkIdentical(mcols(filters[2:1])[,1], 2:1)
checkIdentical(mcols(c(filters,filters))[,1], rep(1:2,2))
checkIdentical(mcols(append(filters,filters))[,1], rep(1:2,2))
}
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