Mercurial > repos > yhoogstrate > edger_with_design_matrix

changeset 37:00b9ceac4332 draft

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Uploaded
author yhoogstrate
date Thu, 22 May 2014 10:10:03 -0400
parents 185effd01633
children 47eadcd9e4b8
files edgeR_Differential_Gene_Expression.xml
diffstat 1 files changed, 8 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/edgeR_Differential_Gene_Expression.xml	Wed May 21 08:50:36 2014 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Thu May 22 10:10:03 2014 -0400
@@ -277,10 +277,17 @@
       ## change e into epsilon somehow
       dev.off()
     }
+    
+    if(output_heatmap_plot != "/dev/null") {
+      pdf(output_heatmap_plot)
+      etable2 <- topTags(lrt, n=100)\$table
+      order <- rownames(etable2)
+      heatmap(t(cpm(dge,normalized.lib.sizes=TRUE),sep="\t",row.names=TRUE,col.names=NA),log=TRUE))
+      dev.off()
+    }
   }
   
   ##output_hierarchical_clustering_plot = args[13]
-  ##output_heatmap_plot                 = args[14]
   
   if(output_RData_obj != "/dev/null") {
     save.image(output_RData_obj)