inst/unitTests/test_esApply.R

In Biobase: Biobase: Base functions for Bioconductor

test_esApply_base <- function() {
    data(sample.ExpressionSet)
    target <- with(pData(sample.ExpressionSet),
                   apply(exprs(sample.ExpressionSet), 1, sum))
    current <- esApply(sample.ExpressionSet, 1, sum)
    checkIdentical(target, current)
}

test_esApply_lexical_scope <- function() {
    data(sample.ExpressionSet)
    f <- function() {
        x <- 0
        function(y) x <<- x + 1
    }
    target <- with(pData(sample.ExpressionSet),
                   apply(exprs(sample.ExpressionSet), 1, f()))
    current <- esApply(sample.ExpressionSet, 1, f())
    checkIdentical(target, current)
}

test_esApply_local_scope <- function() {
    data(sample.ExpressionSet)
    target <- with(pData(sample.ExpressionSet),
                   apply(exprs(sample.ExpressionSet), 1,
                         function(x) {
                             xx <- split(x, sex)
                             mean(xx[[1]]) - mean(xx[[2]])
                         }))
    current <- esApply(sample.ExpressionSet, 1,
                        function(x) {
                            xx <- split(x, sex)
                            mean(xx[[1]]) - mean(xx[[2]])
                        })
    checkIdentical(target, current)

    f <- function(x) {
        xx <- split(x, sex)
        mean(xx[[1]]) - mean(xx[[2]])
    }
    current <- esApply(sample.ExpressionSet, 1, f)
    checkIdentical(target, current)

    f <- function(x, s) {
        xx <- split(x, s)
        mean(xx[[1]])-mean(xx[[2]])
    }
    sex=sample.ExpressionSet[["sex"]]
    current <- esApply(sample.ExpressionSet, 1, f, s=sex)
    checkIdentical(target, current)
}

test_esApply_global_args <- function() {
    data(sample.ExpressionSet)
    f <- function(x, t) t*sum(x)
    target <- with(pData(sample.ExpressionSet),
                   apply(exprs(sample.ExpressionSet), 1, f, 10))
    current <- esApply(sample.ExpressionSet, 1, f, 10)
    checkIdentical(target, current, msg="unnamed global arg")

    current <- esApply(sample.ExpressionSet, 1, f, t=10)
    checkIdentical(target, current, msg="named global arg")
}