Rscript /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/CoMut.4.3421/coMut.R -v -o . --firehose.mode --png --sort.by.mutation.status -a COADREAD -s /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/126340/COADREAD.sig_genes.txt -c /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/126340/COADREAD.patients.counts_and_rates.txt -m /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/126340/COADREAD.final_analysis_set.maf --firehose.mutsig.mutcategs /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/126339/COADREAD.mutcategs.txt
coMut v2.1 -- co-ocurrence of Mutations
Reading significance values.
Reading coverage values.
Reading maf file. 81661 mutations in 228 samples.
282 genes to display...
 q-values:
    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
0.000000 0.005125 0.027500 0.035980 0.062000 0.100000 
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 
