Force expended model

Rfunctions/Stat_Model.R

@@ -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)
   # }