# longtests/testthat/test_old_absentPresent.R In sneumann/xcms: LC-MS and GC-MS Data Analysis

```test_that("present absent sum works", {
xsg <- group(faahko)
a <- length(which(absent(xsg, class="WT", minfrac=0)))
expect_equal(a, 407)
p <- length(which(absent(xsg, class="KO", minfrac=0)))
expect_equal(p, 407)
## Because minfrac = 0.5 translates to >= 3 samples,
## those peak groups with *exactly* 3 Na values
## are counted as both absent and present
p <- length(which(present(xsg, class="WT", minfrac=0.5)))
a <- length(which(absent(xsg , class="WT", minfrac=0.5)))
expect_equal(a+p, 479)
p <- length(which(present(xsg, class="KO", minfrac=0.333333333)))
a <- length(which(absent(xsg,  class="KO", minfrac=0.666666666)))
expect_true(a + p > nrow(groups(xsg)))
## minfrac=0.8,0.2, translate to 1.2 and 4.8 samples
##
p <- length(which(present(xsg, class="WT", minfrac=0.8)))
a <- length(which(absent(xsg, class="WT", minfrac=0.2)))
expect_equal(a+p, 407)
p <- length(which(present(xsg, class="WT", minfrac=0.2)))
a <- length(which(absent(xsg, class="WT", minfrac=0.8)))
expect_equal(a+p, 407)
p <- length(which(present(xsg, class="KO", minfrac=0.75)))
a <- length(which(absent(xsg, class="KO", minfrac=0.25)))
expect_equal(a+p, 407)
p <- length(which(present(xsg, class="KO", minfrac=0.25)))
a <- length(which(absent(xsg, class="KO", minfrac=0.75)))
expect_equal(a+p, 407)
})

##
## Same as above, with fillPeaks()
##
test_that("PresentAbsentSumAfterFillPeaks works", {
xsg <- faahko_grouped_filled
## xsg <- faahko_grouped_filled
a <- length(which(absent(xsg, class="WT", minfrac=0)))
expect_equal(a, 407)
p <- length(which(absent(xsg, class="KO", minfrac=0)))
expect_equal(p, 407)
## Because minfrac = 0.5 translates to >= 3 samples,
## those peak groups with *exactly* 3 Na values
## are counted as both absent and present
p <- length(which(present(xsg, class="WT", minfrac=0.5)))
a <- length(which(absent(xsg , class="WT", minfrac=0.5)))
expect_equal(a+p, 479)
p <- length(which(present(xsg, class="KO", minfrac=0.333333333)))
a <- length(which(absent(xsg,  class="KO", minfrac=0.666666666)))
expect_true(a + p > nrow(groups(xsg)))
## minfrac=0.8,0.2, translate to 1.2 and 4.8 samples
##
p <- length(which(present(xsg, class="WT", minfrac=0.8)))
a <- length(which(absent(xsg, class="WT", minfrac=0.2)))
expect_equal(a+p, 407)
p <- length(which(present(xsg, class="WT", minfrac=0.2)))
a <- length(which(absent(xsg, class="WT", minfrac=0.8)))
expect_equal(a+p, 407)
p <- length(which(present(xsg, class="KO", minfrac=0.75)))
a <- length(which(absent(xsg, class="KO", minfrac=0.25)))
expect_equal(a+p, 407)
p <- length(which(present(xsg, class="KO", minfrac=0.25)))
a <- length(which(absent(xsg, class="KO", minfrac=0.75)))
expect_equal(a+p, 407)
})
```
sneumann/xcms documentation built on June 5, 2024, 4:28 p.m.