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 LUSC -s /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/146704/LUSC.sig_genes.txt -c /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/146704/LUSC.patients.counts_and_rates.txt -m /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/146704/LUSC.final_analysis_set.maf --firehose.mutsig.mutcategs /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/146703/LUSC.mutcategs.txt
coMut v2.2 -- co-ocurrence of Mutations
Reading significance values.
Reading coverage values. 178 samples.
Reading maf file. 62507 mutations in 178 samples.
141 genes to display...
 q-values:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
0.00000 0.00380 0.03300 0.03599 0.05700 0.10000 
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 
