context('ermineJ usage')
# utils::download.file('http://archive.geneontology.org/latest-termdb/go_daily-termdb.rdf-xml.gz',destfile = 'GO.xml.gz',quiet= TRUE)
test_that('ermineJ basic usage',{
annotation = 'Generic_human.txt'
scores <-read.table("testFiles/pValues", header=T, row.names = 1)
result1 = ermineR(annotation = 'testFiles/chip',
geneSetDescription = 'testFiles/go.obo',
scoreColumn = 1,
scores = scores,
output = 'out',
return = TRUE)
testthat::expect_is(result1,'list')
testthat::expect_is(result1$results,'data.frame')
# check column names and integers give the same results
result2 = ermineR(annotation = 'testFiles/chip',
geneSetDescription = 'testFiles/go.obo',
scoreColumn = 'pvalue',
scores = scores,
output = 'out',
return = TRUE)
testthat::expect_identical(result1$results,result2$results)
# test getGoGenes
goGenes = result1 %>% getGoGenes('GO:0051082')
goGenesByName = result1 %>% getGoGenes('unfolded protein binding')
testthat::expect_identical(goGenes, goGenesByName)
})
test_that('setting seed',{
scores <-read.table("testFiles/pValues", header=T, row.names = 1)
set.seed(1)
result1 <- ermineR(annotation = "testFiles/chip",
scores=scores,
scoreColumn = 1,
test="GSR",
stats="precisionRecall",
logTrans=T,
geneSetDescription = 'testFiles/go.obo')
set.seed(1)
result2 <- ermineR(annotation = "testFiles/chip",
scores=scores,
scoreColumn = 1,
test="GSR",
stats="precisionRecall",
logTrans=T,
geneSetDescription = 'testFiles/go.obo')
set.seed(3)
resultDifferent <- ermineR(annotation = "testFiles/chip",
scores=scores,
scoreColumn = 1,
test="GSR",
stats="precisionRecall",
logTrans=T,
geneSetDescription = 'testFiles/go.obo')
testthat::expect_identical(result1$results$Pval,result2$results$Pval)
testthat::expect_false(identical(result1$results$Pval,resultDifferent$results$Pval))
})
testthat::test_that('Reading the european output',{
result = readErmineJOutput('testFiles/europeanResults.tsv')
testthat::expect_is(result$results$Pval,'numeric')
})
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