Debug DESeq worker when the data are large and we want to expand the contrast

Rfunctions/DiagPlot.R

@@ -413,7 +413,7 @@ PCoAPlot_meta <-function (input, dds, group_init, CT,tree,col = c("SpringGreen",
   ## Get the group corresponding to the modalities
   group = group[ind_kept]
   nb = length(unique((group)))
-  group = as.factor(group)
+  group = factor(group, levels = Kval)
   
   if(nlevels(group)!=0 && !is.null(input$PCaxe1) && !is.null(input$PCaxe2))
   { 

Rfunctions/Stat_Model.R

@@ -63,7 +63,8 @@ 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$fitType,parallel = TRUE,minReplicatesForReplace = Inf, modelMatrixType = "expanded")
+     dds = DESeq2shaman::DESeq(dds,test="Wald",fitType=input$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
     }