Commit 663d1592 authored by Amine  GHOZLANE's avatar Amine GHOZLANE

Force expended model

parent e676c88e
Pipeline #14734 canceled with stages
in 42 minutes and 34 seconds
......@@ -63,14 +63,14 @@ Get_dds_object <- function(input,counts,target,design,normFactorsOTU,CT_noNorm,C
# dds <- nbinomWaldTest(dds,modelMatrixType = "expanded")
if(nrow(counts)*nrow(target)>=50000)
{
dds = DESeq2shaman::DESeq(dds,fitType=input$fitType,parallel = TRUE,minReplicatesForReplace = Inf)
dds = DESeq2shaman::DESeq(dds,fitType=input$fitType,parallel = TRUE,minReplicatesForReplace = Inf, modelMatrixType = "expanded")
# try(DESeq(dds,fitType=input$fitType,parallel = TRUE,minReplicatesForReplace = Inf) ->ddstmp,silent = TRUE)
# if(!is.null(ddstmp)) dds = ddstmp
}
if(nrow(counts)*nrow(target)<50000 || is.null(dds))
{
dds <- DESeq2shaman::estimateDispersions(dds, fitType=input$fitType)
dds <- DESeq2shaman::nbinomWaldTest(dds)
dds <- DESeq2shaman::nbinomWaldTest(dds, modelMatrixType = "expanded")
}
# dds <- DESeq(dds,fitType=input$fitType,modelMatrixType = "expanded",parallel = TRUE)
# }
......
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