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context("glmGamPoi")
test_that( "Funcion to create DEXSeqDataSet has the correct inputs", {
skip_if_not_installed("pasilla")
data("pasillaDEXSeqDataSet", package="pasilla")
dxd <- estimateSizeFactors( dxd )
library(glmGamPoi)
expect_message(
dxd_glmgampoi <- estimateDispersions( dxd, fitType="glmGamPoi", BPPARAM=MulticoreParam(2), niter=2 ),
"Parallelization has not been implemented for estimation" )
dxd_glmgampoi <- testForDEU( dxd_glmgampoi, fitType="glmGamPoi" )
expect_s4_class(dxd_glmgampoi, "DEXSeqDataSet")
dxd_default <- estimateDispersions( dxd )
dxd_default <- testForDEU( dxd_default )
expect_s4_class(dxd_default, "DEXSeqDataSet")
dxd_default_p2 <- estimateDispersions( dxd_default, BPPARAM=MulticoreParam(2) )
dxd_default_p2 <- testForDEU( dxd_default_p2, BPPARAM=MulticoreParam(2) )
expect_s4_class(dxd_default, "DEXSeqDataSet")
res_default <- DEXSeqResults( dxd_default )
res_default_p2 <- DEXSeqResults( dxd_default_p2 )
expect_identical(res_default$pvalue, res_default_p2$pvalue)
## res_glmgampoi <- DEXSeqResults(dxd_glmgampoi, independentFiltering=FALSE)
## res_default <- DEXSeqResults(dxd_default, independentFiltering=FALSE)
## table( glmgampoi=res_glmgampoi$padj < 0.1, def=res_default$padj < 0.1 )
dxd_glmgampoi_p2 <- testForDEU( dxd_glmgampoi, fitType="glmGamPoi", BPPARAM=MulticoreParam(3) )
res_glmgampoi <- DEXSeqResults( dxd_glmgampoi )
res_glmgampoi_p2 <- DEXSeqResults( dxd_glmgampoi_p2 )
expect_identical( res_glmgampoi$pvalue, res_glmgampoi_p2$pvalue )
} )
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