Rscript /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/CoMut.7.3708/coMut.R -v -o . --firehose.mode --png --sort.by.mutation.status -a STAD -s /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/160062/STAD.sig_genes.txt -c /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/160062/STAD.patients.counts_and_rates.txt -m /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/160062/STAD.final_analysis_set.maf --firehose.mutsig.mutcategs /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/160061/STAD.mutcategs.txt
coMut v2.2 -- co-ocurrence of Mutations
Reading significance values.
Reading coverage values. 133 samples.
Reading maf file. 76779 mutations in 133 samples.
91 genes to display...
 q-values:
     Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
0.0000000 0.0001275 0.0210000 0.0328200 0.0675000 0.0970000 
Plotting...
  initial image plot
  counts
  q values
  mutations rates
  mutations categories
  legends
null device 
          1 
  initial image plot
  counts
  q values
  mutations rates
  mutations categories
  legends
null device 
          1 
