context('estimation from sample data')
test_that("Basic estimation works",{
temp = data.frame(Gene.Symbol = 'EpicMarker', sample1 = 4,sample2 = 8)
genes = list(epicCellType = 'EpicMarker')
estimates = mgpEstimate(exprData = temp,genes = genes,geneColName = 'Gene.Symbol', geneTransform = NULL)
expect_that(estimates$estimates$epicCellType['sample2'],
is_more_than(estimates$estimates$epicCellType['sample1']))
})
test_that("Basic estimation with tibbles",{
temp = tibble::tibble(Gene.Symbol = 'EpicMarker', sample1 = 4,sample2 = 8)
genes = list(epicCellType = 'EpicMarker')
estimates = mgpEstimate(exprData = temp,genes = genes,geneColName = 'Gene.Symbol', geneTransform = NULL)
expect_that(estimates$estimates$epicCellType['sample2'],
is_more_than(estimates$estimates$epicCellType['sample1']))
})
test_that("Estimation in actual dataset",{
data(mgp_LesnickParkinsonsExp)
data(mgp_LesnickParkinsonsMeta)
data(mouseMarkerGenes)
medExp = mgp_LesnickParkinsonsExp %>% sepExpr() %>% {.[[2]]} %>% unlist %>% median
mgp_LesnickParkinsonsExp = mostVariable(mgp_LesnickParkinsonsExp,threshold = medExp, threshFun= median)
estimates = mgpEstimate(exprData = mgp_LesnickParkinsonsExp,
genes = mouseMarkerGenes$Midbrain,
geneColName = 'Gene.Symbol',
groups = mgp_LesnickParkinsonsMeta$disease)
cells = names(mouseMarkerGenes$Midbrain)
less = sapply(1:length(estimates$estimates),function(i){
wilcox.test(estimates$estimates[[i]][estimates$groups[[i]] %in% "PD"],
estimates$estimates[[i]][estimates$groups[[i]] %in% "Control"],alternative = 'less')$p.value
})
greater = sapply(1:length(estimates$estimates),function(i){
wilcox.test(estimates$estimates[[i]][estimates$groups[[i]] %in% "PD"],
estimates$estimates[[i]][estimates$groups[[i]] %in% "Control"],alternative = 'greater')$p.value
})
expect_that(less[cells %in% 'Dopaminergic'], testthat::is_less_than(0.05))
expect_that(min(less[!cells %in% 'Dopaminergic']), testthat::is_more_than(0.05))
expect_that(min(greater), testthat::is_more_than(0.05))
})
test_that('Wrong parameters',{
data(mgp_LesnickParkinsonsExp)
data(mgp_LesnickParkinsonsMeta)
data(mouseMarkerGenes)
mockMouseGenes = mgp_LesnickParkinsonsExp$Gene.Symbol %>% homologene::human2mouse()
mockMouseData = mgp_LesnickParkinsonsExp[match(mockMouseGenes$humanGene,mgp_LesnickParkinsonsExp$Gene.Symbol),]
mockMouseData$Gene.Symbol = mockMouseGenes$mouseGene
mockMouseData = mockMouseData[!duplicated(mockMouseData$Gene.Symbol),]
testthat::expect_warning(mgpEstimate(exprData = mockMouseData,
genes = mouseMarkerGenes$Midbrain,
geneColName = 'Gene.Symbol',
groups = mgp_LesnickParkinsonsMeta$disease),regexp = 'geneTransform function reduces the number of matches')
})
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