Nothing
context('RMD conversion')
test_that('conversion between log2(RMD) and p-values is seamless', {
# Load data and prepare omicsData objects ------------------------------------
load(system.file('testdata',
'metaboliteData.RData',
package = 'pmartR'
))
mdata <- as.metabData(
e_data = edata,
f_data = fdata,
e_meta = emeta,
edata_cname = 'Metabolite',
fdata_cname = 'SampleID',
emeta_cname = 'MClass'
)
mdata <- edata_transform(
omicsData = mdata,
data_scale = "log"
)
mdata <- group_designation(
omicsData = mdata,
main_effects = "Condition"
)
# Holy RMD conversion tests, Batman! -----------------------------------------
rmd_filta <- rmd_filter(
omicsData = mdata,
metrics = c("MAD", "Skewness", "Correlation")
)
expect_identical(
rmd_conversion(log2rmd = rmd_filta$Log2.md, df = 3),
1 - pchisq(2^(rmd_filta$Log2.md), df = 3)
)
expect_identical(
rmd_conversion(pval = .0001, df = 5),
log(qchisq(1 - 0.0001, df = 5), base = 2)
)
expect_identical(
rmd_conversion(log2rmd = 4.5, df = 3),
1 - pchisq(2^(4.5), df = 3)
)
})
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