context("test identification of core genes for a selected set of taxa")
test_that("test core gene estimation", {
library(dplyr)
data("fullProcessedProfile", package="PhyloProfile")
rankName <- "class"
refTaxon <- "Mammalia"
taxaCore <- c("Mammalia", "Saccharomycetes", "Insecta")
var1Cutoff <- c(0,1)
var2Cutoff <- c(0,1)
percentCutoff <- c(0,1)
coreCoverage <- 100
taxonIDs <- levels(as.factor(fullProcessedProfile$ncbiID))
sortedInputTaxa <- sortInputTaxa(
taxonIDs, rankName, refTaxon, NULL
)
taxaCount <- sortedInputTaxa %>% dplyr::count(supertaxon)
coreGene <- getCoreGene(
rankName,
taxaCore,
fullProcessedProfile,
taxaCount,
var1Cutoff, var2Cutoff,
percentCutoff, coreCoverage
)
expect_true(length(coreGene) == 3)
})
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