context("helper functions for fillPEAKS method")
test_that("all helper functions for fillPEAKS work ", {
# modelPEAKS --------------------------------------------------------------------------------------------------------
## use large study
tmp <- buildTMP(file = large_meta_fname, out_dir = data_dir, rt_err = rt_err)
tmp <- alignPEAKS(tmp, out_dir = data_dir)
tmp <- validPEAKS(tmp, out_dir = data_dir, ncores = 2)
## model rt/mz values for a single peakgr that has missing values
pcs_1 <- tmp@valid[tmp@valid$pcs == 1, "peakid"]
data_2 <- tmp@data[[2]]
peak_miss <- pcs_1[which(!pcs_1%in% data_2[data_2$tmp_peakgr ==1 ,"tmp_peakid" ])]
peaks_ori <- tmp@peaks[[match(peak_miss, names(tmp@peaks))]]
modelPEAKS_out <- modelPEAKS(p = peak_miss,
vars = c("mz", "mzmin", "mzmax", "rt", "rtmin", "rtmax"),
object = tmp
)
expect_true(class(modelPEAKS_out) == "data.frame")
expect_true(nrow(modelPEAKS_out) == nrow(tmp@samples))
expect_equal(
peaks_ori[!is.na(peaks_ori$mz), names(modelPEAKS_out)],
modelPEAKS_out[!is.na(peaks_ori$mz), ]
)
expect_true(all(apply(modelPEAKS_out[is.na(peaks_ori$mz), ], 1:2, is.numeric)))
# smoothVALUE --------------------------------------------------------------------------------------------------------
})
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.