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 ...@@ -63,14 +63,14 @@ Get_dds_object <- function(input,counts,target,design,normFactorsOTU,CT_noNorm,C
# dds <- nbinomWaldTest(dds,modelMatrixType = "expanded") # dds <- nbinomWaldTest(dds,modelMatrixType = "expanded")
if(nrow(counts)*nrow(target)>=50000) 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$fitType,parallel = TRUE,minReplicatesForReplace = Inf) ->ddstmp,silent = TRUE) # try(DESeq(dds,fitType=input$fitType,parallel = TRUE,minReplicatesForReplace = Inf) ->ddstmp,silent = TRUE)
# if(!is.null(ddstmp)) dds = ddstmp # if(!is.null(ddstmp)) dds = ddstmp
} }
if(nrow(counts)*nrow(target)<50000 || is.null(dds)) if(nrow(counts)*nrow(target)<50000 || is.null(dds))
{ {
dds <- DESeq2shaman::estimateDispersions(dds, fitType=input$fitType) dds <- DESeq2shaman::estimateDispersions(dds, fitType=input$fitType)
dds <- DESeq2shaman::nbinomWaldTest(dds) dds <- DESeq2shaman::nbinomWaldTest(dds, modelMatrixType = "expanded")
} }
# dds <- DESeq(dds,fitType=input$fitType,modelMatrixType = "expanded",parallel = TRUE) # dds <- DESeq(dds,fitType=input$fitType,modelMatrixType = "expanded",parallel = TRUE)
# } # }
......
www/Workflow_sh.png

757 KB | W: | H:

www/Workflow_sh.png

644 KB | W: | H:

www/Workflow_sh.png
www/Workflow_sh.png
www/Workflow_sh.png
www/Workflow_sh.png
  • 2-up
  • Swipe
  • Onion skin
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment