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 KIRC -s /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/142839/KIRC.sig_genes.txt -c /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/142839/KIRC.patients.counts_and_rates.txt -m /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/142839/KIRC.final_analysis_set.maf --firehose.mutsig.mutcategs /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/142838/KIRC.mutcategs.txt
coMut v2.1 -- co-ocurrence of Mutations
Reading significance values.
Reading coverage values.
Reading maf file. 25223 mutations in 299 samples.
52 genes to display...
 q-values:
     Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
0.000e+00 5.030e-06 4.300e-03 2.277e-02 3.725e-02 1.000e-01 
Plotting...
  initial image plot
  counts
  q values
  mutations rates
  mutations categories
  legends
  allelic fraction boxplot
null device 
          1 
  initial image plot
  counts
  q values
  mutations rates
  mutations categories
  legends
  allelic fraction boxplot
null device 
          1 
