context('gene selection')
test_that('single run gene selection',{
tempDir = tempfile()
dir.create(tempDir)
data(mgp_sampleProfilesMeta)
data(mgp_sampleProfiles)
data(mpg_sampleRegionHiearchy)
markerCandidates(design = mgp_sampleProfilesMeta,
expression = mgp_sampleProfiles,
outLoc = file.path(tempDir,'markers'),
groupNames = 'CellType',
regionNames = 'region',
PMID = 'PMID',
sampleName = 'sampleName',
replicates = 'replicate',
foldChangeThresh = 10,
minimumExpression = 8,
regionHierarchy = mpg_sampleRegionHiearchy,
geneID = 'Gene.Symbol',
cores = 1,rotate = 0.33)
testthat::expect_that(list.files(file.path(tempDir,'markers')),
testthat::equals(c("All_CellType", "CellType", "Region 2_CellType")))
markers = pickMarkersAll(file.path(tempDir,'markers'))
testthat::expect_that(markers$All_CellType, testthat::equals(list(`Cell A` = "Gene1",
`Cell B` = "Gene2",
`Cell C` = c("Gene3", "Gene4", "Gene5"))))
testthat::expect_that(markers$`Region 2_CellType`, testthat::equals(list(`Cell B` = "Gene2",
`Cell C` = c("Gene3", "Gene4", "Gene5"))))
unlink(tempDir)
})
test_that('gene selection without optional columns and no regions',{
tempDir = tempfile()
dir.create(tempDir)
data(mgp_sampleProfilesMeta)
data(mgp_sampleProfiles)
data(mpg_sampleRegionHiearchy)
mgp_sampleProfilesMeta %<>% dplyr::select(-RegionToParent,-region,-RegionToChildren)
markerCandidates(design = mgp_sampleProfilesMeta,
expression = mgp_sampleProfiles,
outLoc = file.path(tempDir,'markers'),
groupNames = 'CellType',
regionNames = NULL,
PMID = 'PMID',
sampleName = 'sampleName',
replicates = 'replicate',
foldChangeThresh = 10,
minimumExpression = 8,
regionHierarchy = NULL,
geneID = 'Gene.Symbol',
cores = 1,rotate = 0.33)
testthat::expect_that(list.files(file.path(tempDir,'markers')),
testthat::equals("CellType"))
markers = pickMarkersAll(file.path(tempDir,'markers'))
testthat::expect_that(markers$CellType, testthat::equals(list(`Cell A` = "Gene1",
`Cell B` = "Gene2",
`Cell C` = c("Gene3", "Gene4", "Gene5"))))
unlink(tempDir)
})
test_that('file read trial',{
markers =pickMarkers('Cortex_PyramidalDeep')
expect_true(!"Amn" %in% markers$GabaPV)
})
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