test_K2Tworkflow <- function() {
data(K2res)
## Pre-processing
K2check <- K2preproc(K2eSet(K2res))
checkTrue(is(K2check, "K2"), "K2preproc() did not return 'K2' object.\n")
## Taxonomies
K2check <- K2tax(K2check)
checkTrue(is(K2check, "K2"), "K2tax() did not return 'K2' object.\n")
## Dendrograms
dend <- K2dendro(K2check)
checkTrue(is(dend, "dendrogram"), "K2dendro() did not return 'dendrogram'
object.\n")
## Meta-variable tests
K2check <- runTestsMods(K2check,
infoClass=c(
sex="factor",
type="factor1",
score="numeric1"))
checkTrue(is(K2check, "K2"), "runTestsMods() did not return 'K2' object.\n")
## Meta-variable results
mvRes <- getTestsModTable(K2check)
checkTrue(is(mvRes, "data.frame"), "getTestsModTable() did not return
'data.frame'.\n")
## Differential Analysis
K2check <- runDGEmods(K2check)
checkTrue(is(K2check, "K2"), "runDGEmods() did not return 'K2' object.\n")
## DGE results
gRes <- getDGETable(K2check)
checkTrue(is(gRes, "data.frame"), "getDGETable() did not return
'data.frame'.\n")
## Enrichment analysis
K2check <- runGSEmods(K2res,
genesets=K2genesets(K2res))
checkTrue(is(K2check, "K2"), "runGSEmods() did not return 'K2' object.\n")
## Genes 2 pathways
gp <- getGenePathways(K2genesets(K2check))
checkTrue(is(gp, "character"), "runGSEmods() did not return 'character'
vector.\n")
## GSVA
K2check <- runGSVAmods(K2check,
verbose=FALSE)
checkTrue(is(K2check, "K2"), "runGSVAmods() did not return 'K2' object.\n")
## Aggregate GSVA scores
aggList <- list(c("GS12", "GS1", "GS2"))
K2check <- aggregateGSVAscores(aggList, K2check)
checkTrue(is(K2check, "K2"), "aggregateGSVAscores() did not return 'K2'
object.\n")
# Differential pathway analysis
K2check <- runDSSEmods(K2check)
checkTrue(is(K2check, "K2"), "runDSSEmods() did not return 'K2' object.\n")
## Enrichment results
eRes <- getEnrichmentTable(K2check)
checkTrue(is(eRes, "data.frame"), "getEnrichmentTable() did not return
'data.frame'.\n")
## Dashboard
K2dashboard(K2res, output_dir=tempdir())
K2resDir <- list.files(tempdir(), pattern="K2Taxonomer_",
full.names=TRUE)[[1]]
checkTrue(file.exists(file.path(K2resDir, "about.md")),
"K2dashboard() didn't write files.")
checkTrue(file.exists(file.path(K2resDir, "K2results.rds")),
"K2dashboard() didn't write files.")
checkTrue(file.exists(file.path(K2resDir, "K2Taxonomer.Rmd")),
"K2dashboard() didn't write files.")
## Wrapper
K2check <- runK2Taxonomer(K2eSet(K2res),
genesets=K2genesets(K2res),
infoClass=c(
sex="factor",
type="factor1",
score="numeric1")
)
checkTrue(is(K2check, "K2"),
"runK2Taxonomer() did not return 'K2' object.\n")
}
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