Commit 3f77e0b2 authored by Amine  GHOZLANE's avatar Amine GHOZLANE
Browse files

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

parent 310bfc18
Pipeline #15159 passed with stage
in 8 minutes and 17 seconds
...@@ -413,7 +413,7 @@ PCoAPlot_meta <-function (input, dds, group_init, CT,tree,col = c("SpringGreen", ...@@ -413,7 +413,7 @@ PCoAPlot_meta <-function (input, dds, group_init, CT,tree,col = c("SpringGreen",
## Get the group corresponding to the modalities ## Get the group corresponding to the modalities
group = group[ind_kept] group = group[ind_kept]
nb = length(unique((group))) 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)) if(nlevels(group)!=0 && !is.null(input$PCaxe1) && !is.null(input$PCaxe2))
{ {
......
...@@ -63,7 +63,8 @@ Get_dds_object <- function(input,counts,target,design,normFactorsOTU,CT_noNorm,C ...@@ -63,7 +63,8 @@ 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$fitType,parallel = TRUE,minReplicatesForReplace = Inf, modelMatrixType = "expanded") dds = DESeq2shaman::DESeq(dds,test="Wald",fitType=input$fitType,parallel = TRUE,minReplicatesForReplace = Inf, modelMatrixType = "expanded")
#
# try(DESeq(dds,fitType=input$fitType,parallel = TRUE,minReplicatesForReplace = Inf) ->ddstmp,silent = TRUE) # try(DESeq(dds,fitType=input$fitType,parallel = TRUE,minReplicatesForReplace = Inf) ->ddstmp,silent = TRUE)
# if(!is.null(ddstmp)) dds = ddstmp # if(!is.null(ddstmp)) dds = ddstmp
} }
......
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