Removed all the glimma stuff

uzh · Oct 22, 2021 · fd84c58 · fd84c58
1 parent 8a459ab
commit fd84c58
Showing 1 changed file with 0 additions and 71 deletions.
diff --git a/R/app-deseq2TwoGroups.R b/R/app-deseq2TwoGroups.R
@@ -41,77 +41,6 @@ ezMethodDeseq2 = function(input=NA, output=NA, param=NA){
                         row.names = rownames(deResult),
                         check.names = FALSE)
 
-  glimmaResults <- list()
-  glimmaResults[["res"]] <- results(
-    object = dds, 
-    contrast = c("grouping", param$sampleGroup, param$refGroup))
-  glimmaResults[["status"]] <- as.numeric(
-    glimmaResults[["res"]]$pvalue < param$pValueHighlightThresh & 
-    abs(glimmaResults[["res"]]$log2FoldChange) > param$log2RatioHighlightThresh)
-  glimmaResults[["counts"]] <- as.data.frame(
-    assay(varianceStabilizingTransformation(dds)))
-  if (!is.null(param$grouping2Name)) {
-    glimmaResults[["counts"]] <- limma::removeBatchEffect(
-      glimmaResults[["counts"]], dataset[[param$grouping2Name]]
-    )
-  }
-  glimmaResults[["samples"]] <- colnames(dds)
-  glimmaResults[["anno"]] <- seqAnno[, c("gene_id", "gene_name", "description")]
-  glimmaResults[["anno"]]$GeneID <- glimmaResults[["anno"]]$gene_id
-  glimmaResults[["groups"]] <- colData(dds)$grouping
-  glimmaResults[["resDF"]] <- as.data.frame(glimmaResults[["res"]])
-  glimmaResults[["resDF"]] <- glimmaResults[["resDF"]][
-    rownames(glimmaResults[["resDF"]]) %in% 
-      seqAnno$gene_id[seqAnno$usedInTest == TRUE], ]
-  glimmaResults[["countsXY"]] <- glimmaResults[["counts"]][
-    rownames(glimmaResults[["counts"]]) %in% 
-      rownames(glimmaResults[["resDF"]]), ]
-  glimmaResults[["statusXY"]] <- as.numeric(
-    glimmaResults[["resDF"]]$pvalue < 
-      param$pValueHighlightThresh & 
-      abs(glimmaResults[["resDF"]]$log2FoldChange) > 
-      param$log2RatioHighlightThresh)
-  glimmaResults[["annoXY"]] <- glimmaResults[["anno"]][
-    glimmaResults[["anno"]]$gene_id %in% 
-      rownames(glimmaResults[["resDF"]]), ]
-
-  #Glimma::glMDPlot(
-  #  x = glimmaResults[["res"]],
-  #  counts = glimmaResults[["counts"]], 
-  #  anno = glimmaResults[["anno"]], 
-  #  groups = glimmaResults[["groups"]], 
-  #  samples = glimmaResults[["samples"]],
-  #  status = glimmaResults[["status"]], 
-  #  main = param$comparison, 
-  #  html = paste0(param$comparison, "_MA"), 
-  #  side.main = "gene_name",
-  #  launch = FALSE)
-
-  #Glimma::glXYPlot(
-  #  x = glimmaResults[["resDF"]]$log2FoldChange,
-  #  y = -log10(glimmaResults[["resDF"]]$pvalue), 
-  #  xlab = "Log2FC",
-  #  ylab = "-log10 p-value",
-  #  counts = glimmaResults[["countsXY"]],
-  #  groups = glimmaResults[["groups"]],
-  #  samples = glimmaResults[["samples"]], 
-  #  status = glimmaResults[["statusXY"]],
-  #  anno = glimmaResults[["annoXY"]],
-  #  main = param$comparison, 
-  #  html = paste0(param$comparison, "_Volcano"), 
-  #  launch = FALSE)
-
-  #Glimma::glMDSPlot(
-  #  x = glimmaResults[["counts"]], 
-  #  top = 2000, 
-  #  labels = glimmaResults[["samples"]],
-  #  groups = glimmaResults[["groups"]],
-  #  main = param$comparison,
-  #  html = paste0(param$comparison, "_MDS"), 
-  #  launch = FALSE)
-
-  #system(paste0("zip -r ", param$comparison, "_glimma-plots glimma-plots"))
-
   makeRmdReport(output=output, param=param, deResult=deResult, rmdFile="twoGroups.Rmd", reportTitle = param$comparison)
   return("Success")
 }