library(testthat)
library(ZicoSeq)
library(GUniFrac)
context('Just test ZicoSeq function')
test_that('Checking ZicoSeq Results',{
data("throat.otu.tab")
data("throat.meta")
set.seed(123)
comm <- t(throat.otu.tab)
meta.dat <- throat.meta
zico.obj <- ZicoSeq(meta.dat = meta.dat, comm = comm, grp.name = 'SmokingStatus', adj.name = 'Sex',
# Filtering criterion
prev.filter = 0.1, abund.filter = 10, min.prop = 0,
# Winsorization to replace outliers
is.winsor = TRUE, winsor.qt = 0.97,
# Posterior sampling
is.prior = TRUE, prior.dist = c('BetaMix'), post.method = c('sample'), post.sample.no = 25,
# Link functions
link.func = list(function (x) x^0.25, function (x) x^0.5, function (x) x^0.75), stats.combine.func = max,
# Permutation
perm.no = 99, strata = NULL,
# Multiple stage normalization
stage.no = 6, topK = NULL, stage.fdr = 0.75, stage.max.pct = 0.50,
# Tree-based FDR control and family-wise error rate control
is.fwer = FALSE, is.tree.fdr = FALSE, tree = NULL,
verbose = TRUE, return.comm = FALSE, return.perm.F = FALSE)
output <- which(zico.obj$p.adj.fdr <= 0.1)
expect(output,c(`3227` = 7L, `5496` = 65L, `2300` = 92L, `2831` = 96L, `2434` = 99L,
`2893` = 101L, `1280` = 106L, `4363` = 115L, `1490` = 126L, `411` = 127L,
`4703` = 131L, `3954` = 150L, `3538` = 176L))
})
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