127 lines
7.1 KiB
R
127 lines
7.1 KiB
R
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test_RleViews <- function() {
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empty <- Views(Rle(), IRanges())
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checkIdentical(empty, new("RleViews"))
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checkIdentical(list(), viewApply(empty, min))
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checkIdentical(integer(0), viewMins(empty))
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checkIdentical(integer(0), viewMaxs(empty))
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checkIdentical(integer(0), viewSums(empty))
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checkIdentical(numeric(0), viewMeans(empty))
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checkIdentical(integer(0), viewWhichMins(empty))
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checkIdentical(integer(0), viewWhichMaxs(empty))
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checkIdentical(IRanges(), viewRangeMins(empty))
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checkIdentical(IRanges(), viewRangeMaxs(empty))
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x <- rep(c(1L, 3L, NA, 7L, 9L), 1:5)
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xRle <- Rle(x)
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xRleViewsUntrimmed <- Views(xRle, IRanges(start = c(1,1), width = c(0,20)))
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checkIdentical(c(Inf, 1), suppressWarnings(viewApply(xRleViewsUntrimmed, min, na.rm = TRUE)))
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checkIdentical(c(2147483647L, 1L),
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viewMins(xRleViewsUntrimmed, na.rm = TRUE))
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checkIdentical(viewMins(xRleViewsUntrimmed, na.rm = TRUE),
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min(xRleViewsUntrimmed, na.rm = TRUE))
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checkIdentical(c(-2147483647L, 9L),
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viewMaxs(xRleViewsUntrimmed, na.rm = TRUE))
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checkIdentical(viewMaxs(xRleViewsUntrimmed, na.rm = TRUE),
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max(xRleViewsUntrimmed, na.rm = TRUE))
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checkIdentical(c(0L, 80L), viewSums(xRleViewsUntrimmed, na.rm = TRUE))
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checkIdentical(viewSums(xRleViewsUntrimmed, na.rm = TRUE),
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sum(xRleViewsUntrimmed, na.rm = TRUE))
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checkIdentical(c(NaN, 20/3), viewMeans(xRleViewsUntrimmed, na.rm = TRUE))
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checkIdentical(viewMeans(xRleViewsUntrimmed, na.rm = TRUE),
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mean(xRleViewsUntrimmed, na.rm = TRUE))
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checkIdentical(c(NA_integer_, 1L),
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viewWhichMins(xRleViewsUntrimmed, na.rm = TRUE))
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checkIdentical(viewWhichMins(xRleViewsUntrimmed, na.rm = TRUE),
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which.min(xRleViewsUntrimmed))
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checkIdentical(c(NA_integer_, 11L),
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viewWhichMaxs(xRleViewsUntrimmed, na.rm = TRUE))
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checkIdentical(viewWhichMaxs(xRleViewsUntrimmed, na.rm = TRUE),
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which.max(xRleViewsUntrimmed))
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checkException(max(xRleViewsUntrimmed, xRleViewsUntrimmed, na.rm = TRUE),
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silent = TRUE)
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xRleViews <-
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Views(xRle, start = c(1, 3, 5, 7, 9), end = c(1, 13, 11, 10, 9), names = letters[1:5])
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xList <-
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lapply(structure(seq_len(length(xRleViews)), names = letters[1:5]),
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function(i) window(x, start = start(xRleViews)[i], end = end(xRleViews)[i]))
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checkIdentical(letters[1:5], names(viewApply(xRleViews, min)))
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checkIdentical(letters[1:5], names(viewMins(xRleViews)))
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checkIdentical(letters[1:5], names(viewMaxs(xRleViews)))
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checkIdentical(letters[1:5], names(viewSums(xRleViews)))
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checkIdentical(letters[1:5], names(viewMeans(xRleViews)))
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checkIdentical(letters[1:5], names(viewWhichMins(xRleViews)))
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checkIdentical(letters[1:5], names(viewWhichMaxs(xRleViews)))
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checkIdentical(letters[1:5], names(viewRangeMins(xRleViews, na.rm = TRUE)))
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checkIdentical(letters[1:5], names(viewRangeMaxs(xRleViews, na.rm = TRUE)))
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checkEqualsNumeric(sapply(xList, min), viewMins(xRleViews))
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checkEqualsNumeric(sapply(xList, min), viewApply(xRleViews, min))
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checkEqualsNumeric(sapply(xList, min, na.rm = TRUE),
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viewMins(xRleViews, na.rm = TRUE))
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checkEqualsNumeric(sapply(xList, min, na.rm = TRUE),
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viewApply(xRleViews, min, na.rm = TRUE))
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checkEqualsNumeric(sapply(xList, max), viewMaxs(xRleViews))
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checkEqualsNumeric(sapply(xList, max), viewApply(xRleViews, max))
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checkEqualsNumeric(sapply(xList, max, na.rm = TRUE),
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viewMaxs(xRleViews, na.rm = TRUE))
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checkEqualsNumeric(sapply(xList, max, na.rm = TRUE),
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viewApply(xRleViews, max, na.rm = TRUE))
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checkEqualsNumeric(sapply(xList, sum), viewSums(xRleViews))
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checkEqualsNumeric(sapply(xList, mean), viewMeans(xRleViews))
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checkEqualsNumeric(sapply(xList, sum), viewApply(xRleViews, sum))
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checkEqualsNumeric(sapply(xList, sum, na.rm = TRUE),
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viewSums(xRleViews, na.rm = TRUE))
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checkEqualsNumeric(sapply(xList, mean, na.rm = TRUE),
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viewMeans(xRleViews, na.rm = TRUE))
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checkEqualsNumeric(sapply(xList, sum, na.rm = TRUE),
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viewApply(xRleViews, sum, na.rm = TRUE))
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y <- rep(c(1.2, 3.4, NA, 7.8, 9.0), 1:5)
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yRle <- Rle(y)
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yRleViewsUntrimmed <- Views(yRle, IRanges(start = c(1,1), width = c(0,20)))
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checkIdentical(c(Inf, 1.2), suppressWarnings(viewApply(yRleViewsUntrimmed, min, na.rm = TRUE)))
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checkIdentical(c(Inf, 1.2), viewMins(yRleViewsUntrimmed, na.rm = TRUE))
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checkIdentical(c(-Inf, 9), viewMaxs(yRleViewsUntrimmed, na.rm = TRUE))
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checkIdentical(c(0, 84.2), viewSums(yRleViewsUntrimmed, na.rm = TRUE))
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checkIdentical(c(NaN, 84.2/12), viewMeans(yRleViewsUntrimmed, na.rm = TRUE))
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checkIdentical(c(NA_integer_, 1L), viewWhichMins(yRleViewsUntrimmed, na.rm = TRUE))
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checkIdentical(c(NA_integer_, 11L), viewWhichMaxs(yRleViewsUntrimmed, na.rm = TRUE))
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yRleViews <- Views(yRle, start = c(1, 3, 5, 7, 9), end = c(1, 13, 11, 10, 9))
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yList <-
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lapply(seq_len(length(yRleViews)),
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function(i) window(y, start = start(yRleViews)[i], end = end(yRleViews)[i]))
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checkEqualsNumeric(sapply(yList, min), viewMins(yRleViews))
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checkEqualsNumeric(sapply(yList, min), viewApply(yRleViews, min))
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checkEqualsNumeric(sapply(yList, min, na.rm = TRUE), viewMins(yRleViews, na.rm = TRUE))
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checkEqualsNumeric(sapply(yList, min, na.rm = TRUE), viewApply(yRleViews, min, na.rm = TRUE))
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checkEqualsNumeric(sapply(yList, max), viewMaxs(yRleViews))
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checkEqualsNumeric(sapply(yList, max), viewApply(yRleViews, max))
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checkEqualsNumeric(sapply(yList, max, na.rm = TRUE), viewMaxs(yRleViews, na.rm = TRUE))
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checkEqualsNumeric(sapply(yList, max, na.rm = TRUE), viewApply(yRleViews, max, na.rm = TRUE))
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checkEqualsNumeric(sapply(yList, sum), viewSums(yRleViews))
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checkEqualsNumeric(sapply(yList, mean), viewMeans(yRleViews))
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checkEqualsNumeric(sapply(yList, sum), viewApply(yRleViews, sum))
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checkEqualsNumeric(sapply(yList, sum, na.rm = TRUE), viewSums(yRleViews, na.rm = TRUE))
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checkEqualsNumeric(sapply(yList, mean, na.rm = TRUE), viewMeans(yRleViews, na.rm = TRUE))
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checkEqualsNumeric(sapply(yList, sum, na.rm = TRUE), viewApply(yRleViews, sum, na.rm = TRUE))
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z <- rep(c(1+1i, 3.4-1i, NA, 7.8+3i, 9.0-2i), 1:5)
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zRle <- Rle(z)
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zRleViews <- Views(zRle, start = c(1, 3, 5, 7, 9), end = c(1, 13, 11, 10, 9))
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zList <-
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lapply(seq_len(length(zRleViews)),
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function(i) window(z, start = start(zRleViews)[i], end = end(zRleViews)[i]))
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checkEqualsNumeric(sapply(zList, sum), viewSums(zRleViews))
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checkEqualsNumeric(sapply(zList, mean), viewMeans(zRleViews))
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checkEqualsNumeric(sapply(zList, sum), viewApply(zRleViews, sum))
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checkEqualsNumeric(sapply(zList, sum, na.rm = TRUE), viewSums(zRleViews, na.rm = TRUE))
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checkEqualsNumeric(sapply(zList, mean, na.rm = TRUE), viewMeans(zRleViews, na.rm = TRUE))
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checkEqualsNumeric(sapply(zList, sum, na.rm = TRUE), viewApply(zRleViews, sum, na.rm = TRUE))
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}
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