/usr/lib/R/site-library/Biostrings/unitTests/test_twoWayAlphabetFrequency.R is in r-bioc-biostrings 2.42.1-1.
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 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 | test_twoWayAlphabetFrequency <- function() {
## Equivalence classes:
##
## x, y:
## - length [Set]: (different length), zero, length one, length > one
## - string length: (inconsistent lengths), zero, same, [Set] varying
## - content: some matches, every cell
## - types: XString, DNAString, XStringSet, DNAStringSet, (different)
##
## as.prob: TRUE, FALSE, (NA), (not logical)
## baseOnly [DNA]: TRUE, FALSE, (NA), (not logical)
## collapse [Set]: TRUE, FALSE, (NA), (not logical)
library(Biostrings)
library(RUnit)
testMatrix <-
function(x, y, v, as.prob = FALSE, baseOnly = FALSE, collapse = FALSE) {
x.alphabet <- Biostrings:::xscodes(x, baseOnly=baseOnly)
y.alphabet <- Biostrings:::xscodes(y, baseOnly=baseOnly)
dim <- c(length(x.alphabet), length(y.alphabet))
dimnames <- list(names(x.alphabet), names(y.alphabet))
if (baseOnly) {
if (!is.null(dimnames[[1]]))
dimnames[[1]] <- c(dimnames[[1]], "other")
if (!is.null(dimnames[[2]]))
dimnames[[2]] <- c(dimnames[[2]], "other")
dim <- dim + 1L
}
mode(v) <- "integer"
if (as.prob) {
if (collapse)
v <- v / sum(v)
else v <- v / rep(nchar(x), each = prod(dim(v)))
}
if (is(x, "XStringSet") || is(y, "XStringSet")) {
dimnames <- c(dimnames, list(NULL))
dim <- c(dim, nchar(x))
}
a <- array(0L, dim = dim, dimnames = dimnames)
if (is.null(rownames(a))) {
x.ind <- as.integer(sapply(rownames(v), charToRaw)) + 1L
} else {
x.ind <- rownames(v)
}
if (is.null(colnames(a))) {
y.ind <- as.integer(sapply(rownames(v), charToRaw)) + 1L
} else {
y.ind <- rownames(v)
}
if (length(dim(a)) == 3)
a[x.ind,y.ind,] <- v
else a[x.ind,y.ind] <- v
a
}
some.a <- "ACGTACGTACGT"
some.b <- "ACGTTGCAGGGA"
some.mat <- rbind(A = c(1, 0, 1, 1),
C = c(0, 1, 2, 0),
G = c(0, 1, 2, 0),
T = c(2, 0, 0, 1))
## CASE: different nchar, DNAString
checkException(twoWayAlphabetFrequency(DNAString("ACGT"), DNAString("ACG")),
silent = TRUE)
## CASE: zero, DNAString
x <- y <- DNAString("")
checkIdentical(testMatrix(x, y, 0L), twoWayAlphabetFrequency(x, y))
## CASE: some, XString, FALSE
x <- BString(some.a)
y <- BString(some.b)
truth <- testMatrix(x, y, some.mat)
checkIdentical(truth, twoWayAlphabetFrequency(x, y))
## CASE: some, XString, TRUE
truth <- truth / sum(truth)
checkIdentical(truth, twoWayAlphabetFrequency(x, y, as.prob = TRUE))
## CASE: XString, DNAString
x <- BString(some.a)
y <- DNAString(some.b)
truth <- testMatrix(x, y, some.mat)
checkIdentical(truth, twoWayAlphabetFrequency(x, y))
## CASE: XString, DNAString, baseOnly = TRUE
truth <- testMatrix(x, y, some.mat, baseOnly = TRUE)
checkIdentical(truth, twoWayAlphabetFrequency(x, y, baseOnly = TRUE))
## CASE: some, DNAString, NA, FALSE
x <- DNAString(some.a)
y <- DNAString(some.b)
checkException(twoWayAlphabetFrequency(x, y, as.prob = NA),
silent = TRUE)
## CASE: some, DNAString, "foo", FALSE
checkException(twoWayAlphabetFrequency(x, y, as.prob = "foo"),
silent = TRUE)
## CASE: some, DNAString, FALSE, NA
checkException(twoWayAlphabetFrequency(x, y, baseOnly = NA),
silent = TRUE)
## CASE: some, DNAString, FALSE, "foo"
checkException(twoWayAlphabetFrequency(x, y, baseOnly = "foo"),
silent = TRUE)
## CASE: some, DNAString, TRUE, FALSE
truth <- testMatrix(x, y, some.mat, as.prob = TRUE)
checkIdentical(truth, twoWayAlphabetFrequency(x, y, as.prob = TRUE))
## CASE: some, DNAString, FALSE, TRUE
truth <- testMatrix(x, y, some.mat, baseOnly = TRUE)
checkIdentical(truth, twoWayAlphabetFrequency(x, y, baseOnly = TRUE))
## CASE: some, DNAString, TRUE, TRUE
## CASE: every, DNAString, FALSE, FALSE
## CASE: DNAStringSet, DNAString
## CASE: different length, DNAStringSet
## CASE: different length, XStringSet
## CASE: different widths, DNAStringSet
## CASE: different widths, XStringSet
## CASE: length==0, DNAString, FALSE, FALSE, FALSE
## CASE: length==0, DNAString, FALSE, FALSE, TRUE
## CASE: length==1, some, DNAStringSet, FALSE, FALSE, FALSE
## CASE: length==1, some, DNAStringSet, FALSE, FALSE, TRUE
## CASE: length >1, some, XStringSet, FALSE, , FALSE
## CASE: length >1, some, XStringSet, TRUE, , FALSE
## CASE: length >1, some, XStringSet, FALSE, , TRUE
## CASE: length >1, some, XStringSet, TRUE, , TRUE
## CASE: length >1, some, DNAStringSet, FALSE, FALSE, NA
## CASE: length >1, some, DNAStringSet, FALSE, FALSE, "foo"
## CASE: length >1, some, DNAStringSet, FALSE, FALSE, FALSE
## CASE: length >1, some, DNAStringSet, TRUE, FALSE, FALSE
## CASE: length >1, some, DNAStringSet, FALSE, FALSE, TRUE
## CASE: length >1, some, DNAStringSet, TRUE, FALSE, TRUE
## CASE: length >1, some, DNAStringSet, FALSE, TRUE, FALSE
## CASE: length >1, some, DNAStringSet, TRUE, TRUE, FALSE
## CASE: length >1, some, DNAStringSet, FALSE, TRUE, TRUE
## CASE: length >1, some, DNAStringSet, TRUE, TRUE, TRUE
## CASE: XString, DNAStringSet
## CASE: XStringSet, DNAString
}
|