inst/unitTests/test_RleViews.R

In Bioconductor/IRanges: Foundation of integer range manipulation in Bioconductor

test_RleViews <- function() {
    empty <- Views(Rle(), IRanges())
    checkIdentical(empty, new("RleViews"))
    checkIdentical(list(), viewApply(empty, min))
    checkIdentical(integer(0), viewMins(empty))
    checkIdentical(integer(0), viewMaxs(empty))
    checkIdentical(integer(0), viewSums(empty))
    checkIdentical(numeric(0), viewMeans(empty))
    checkIdentical(integer(0), viewWhichMins(empty))
    checkIdentical(integer(0), viewWhichMaxs(empty))
    checkIdentical(IRanges(), viewRangeMins(empty))
    checkIdentical(IRanges(), viewRangeMaxs(empty))

    x <- rep(c(1L, 3L, NA, 7L, 9L), 1:5)
    xRle <- Rle(x)

    xRleViewsUntrimmed <- Views(xRle, IRanges(start = c(1,1), width = c(0,20)))
    checkIdentical(c(Inf, 1), suppressWarnings(viewApply(xRleViewsUntrimmed, min, na.rm = TRUE)))
    checkIdentical(c(2147483647L, 1L),
                   viewMins(xRleViewsUntrimmed, na.rm = TRUE))
    checkIdentical(viewMins(xRleViewsUntrimmed, na.rm = TRUE),
                   min(xRleViewsUntrimmed, na.rm = TRUE))
    checkIdentical(c(-2147483647L, 9L),
                   viewMaxs(xRleViewsUntrimmed, na.rm = TRUE))
    checkIdentical(viewMaxs(xRleViewsUntrimmed, na.rm = TRUE),
                   max(xRleViewsUntrimmed, na.rm = TRUE))
    checkIdentical(c(0L, 80L), viewSums(xRleViewsUntrimmed, na.rm = TRUE))
    checkIdentical(viewSums(xRleViewsUntrimmed, na.rm = TRUE),
                   sum(xRleViewsUntrimmed, na.rm = TRUE))
    checkIdentical(c(NaN, 20/3), viewMeans(xRleViewsUntrimmed, na.rm = TRUE))
    checkIdentical(viewMeans(xRleViewsUntrimmed, na.rm = TRUE),
                   mean(xRleViewsUntrimmed, na.rm = TRUE))
    checkIdentical(c(NA_integer_, 1L),
                   viewWhichMins(xRleViewsUntrimmed, na.rm = TRUE))
    checkIdentical(viewWhichMins(xRleViewsUntrimmed, na.rm = TRUE),
                   which.min(xRleViewsUntrimmed))
    checkIdentical(c(NA_integer_, 11L),
                   viewWhichMaxs(xRleViewsUntrimmed, na.rm = TRUE))
    checkIdentical(viewWhichMaxs(xRleViewsUntrimmed, na.rm = TRUE),
                   which.max(xRleViewsUntrimmed))

    checkException(max(xRleViewsUntrimmed, xRleViewsUntrimmed, na.rm = TRUE),
                   silent = TRUE)
    
    xRleViews <-
      Views(xRle, start = c(1, 3, 5, 7, 9), end = c(1, 13, 11, 10, 9), names = letters[1:5])
    xList <-
      lapply(structure(seq_len(length(xRleViews)), names = letters[1:5]),
             function(i) window(x, start = start(xRleViews)[i], end = end(xRleViews)[i]))

    checkIdentical(letters[1:5], names(viewApply(xRleViews, min)))
    checkIdentical(letters[1:5], names(viewMins(xRleViews)))
    checkIdentical(letters[1:5], names(viewMaxs(xRleViews)))
    checkIdentical(letters[1:5], names(viewSums(xRleViews)))
    checkIdentical(letters[1:5], names(viewMeans(xRleViews)))
    checkIdentical(letters[1:5], names(viewWhichMins(xRleViews)))
    checkIdentical(letters[1:5], names(viewWhichMaxs(xRleViews)))
    checkIdentical(letters[1:5], names(viewRangeMins(xRleViews, na.rm = TRUE)))
    checkIdentical(letters[1:5], names(viewRangeMaxs(xRleViews, na.rm = TRUE)))

    checkEqualsNumeric(sapply(xList, min), viewMins(xRleViews))
    checkEqualsNumeric(sapply(xList, min), viewApply(xRleViews, min))
    checkEqualsNumeric(sapply(xList, min, na.rm = TRUE),
                       viewMins(xRleViews, na.rm = TRUE))
    checkEqualsNumeric(sapply(xList, min, na.rm = TRUE),
                       viewApply(xRleViews, min, na.rm = TRUE))
    checkEqualsNumeric(sapply(xList, max), viewMaxs(xRleViews))
    checkEqualsNumeric(sapply(xList, max), viewApply(xRleViews, max))
    checkEqualsNumeric(sapply(xList, max, na.rm = TRUE),
                       viewMaxs(xRleViews, na.rm = TRUE))
    checkEqualsNumeric(sapply(xList, max, na.rm = TRUE),
                       viewApply(xRleViews, max, na.rm = TRUE))
    checkEqualsNumeric(sapply(xList, sum), viewSums(xRleViews))
    checkEqualsNumeric(sapply(xList, mean), viewMeans(xRleViews))
    checkEqualsNumeric(sapply(xList, sum), viewApply(xRleViews, sum))
    checkEqualsNumeric(sapply(xList, sum, na.rm = TRUE),
                       viewSums(xRleViews, na.rm = TRUE))
    checkEqualsNumeric(sapply(xList, mean, na.rm = TRUE),
                       viewMeans(xRleViews, na.rm = TRUE))
    checkEqualsNumeric(sapply(xList, sum, na.rm = TRUE),
                       viewApply(xRleViews, sum, na.rm = TRUE))

    y <- rep(c(1.2, 3.4, NA, 7.8, 9.0), 1:5)
    yRle <- Rle(y)

    yRleViewsUntrimmed <- Views(yRle, IRanges(start = c(1,1), width = c(0,20)))
    checkIdentical(c(Inf, 1.2), suppressWarnings(viewApply(yRleViewsUntrimmed, min, na.rm = TRUE)))
    checkIdentical(c(Inf, 1.2), viewMins(yRleViewsUntrimmed, na.rm = TRUE))
    checkIdentical(c(-Inf, 9), viewMaxs(yRleViewsUntrimmed, na.rm = TRUE))
    checkIdentical(c(0, 84.2), viewSums(yRleViewsUntrimmed, na.rm = TRUE))
    checkIdentical(c(NaN, 84.2/12), viewMeans(yRleViewsUntrimmed, na.rm = TRUE))
    checkIdentical(c(NA_integer_, 1L), viewWhichMins(yRleViewsUntrimmed, na.rm = TRUE))
    checkIdentical(c(NA_integer_, 11L), viewWhichMaxs(yRleViewsUntrimmed, na.rm = TRUE))

    yRleViews <- Views(yRle, start = c(1, 3, 5, 7, 9), end = c(1, 13, 11, 10, 9))
    yList <-
      lapply(seq_len(length(yRleViews)),
             function(i) window(y, start = start(yRleViews)[i], end = end(yRleViews)[i]))
    checkEqualsNumeric(sapply(yList, min), viewMins(yRleViews))
    checkEqualsNumeric(sapply(yList, min), viewApply(yRleViews, min))
    checkEqualsNumeric(sapply(yList, min, na.rm = TRUE), viewMins(yRleViews, na.rm = TRUE))
    checkEqualsNumeric(sapply(yList, min, na.rm = TRUE), viewApply(yRleViews, min, na.rm = TRUE))
    checkEqualsNumeric(sapply(yList, max), viewMaxs(yRleViews))
    checkEqualsNumeric(sapply(yList, max), viewApply(yRleViews, max))
    checkEqualsNumeric(sapply(yList, max, na.rm = TRUE), viewMaxs(yRleViews, na.rm = TRUE))
    checkEqualsNumeric(sapply(yList, max, na.rm = TRUE), viewApply(yRleViews, max, na.rm = TRUE))
    checkEqualsNumeric(sapply(yList, sum), viewSums(yRleViews))
    checkEqualsNumeric(sapply(yList, mean), viewMeans(yRleViews))
    checkEqualsNumeric(sapply(yList, sum), viewApply(yRleViews, sum))
    checkEqualsNumeric(sapply(yList, sum, na.rm = TRUE), viewSums(yRleViews, na.rm = TRUE))
    checkEqualsNumeric(sapply(yList, mean, na.rm = TRUE), viewMeans(yRleViews, na.rm = TRUE))
    checkEqualsNumeric(sapply(yList, sum, na.rm = TRUE), viewApply(yRleViews, sum, na.rm = TRUE))

    z <- rep(c(1+1i, 3.4-1i, NA, 7.8+3i, 9.0-2i), 1:5)
    zRle <- Rle(z)
    zRleViews <- Views(zRle, start = c(1, 3, 5, 7, 9), end = c(1, 13, 11, 10, 9))
    zList <-
      lapply(seq_len(length(zRleViews)),
             function(i) window(z, start = start(zRleViews)[i], end = end(zRleViews)[i]))
    checkEqualsNumeric(sapply(zList, sum), viewSums(zRleViews))
    checkEqualsNumeric(sapply(zList, mean), viewMeans(zRleViews))
    checkEqualsNumeric(sapply(zList, sum), viewApply(zRleViews, sum))
    checkEqualsNumeric(sapply(zList, sum, na.rm = TRUE), viewSums(zRleViews, na.rm = TRUE))
    checkEqualsNumeric(sapply(zList, mean, na.rm = TRUE), viewMeans(zRleViews, na.rm = TRUE))
    checkEqualsNumeric(sapply(zList, sum, na.rm = TRUE), viewApply(zRleViews, sum, na.rm = TRUE))
}