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 LAML -s /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/130523/LAML.sig_genes.txt -c /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/130523/LAML.patients.counts_and_rates.txt -m /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/130523/LAML.final_analysis_set.maf --firehose.mutsig.mutcategs /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/130522/LAML.mutcategs.txt
coMut v2.1 -- co-ocurrence of Mutations
Reading significance values.
Reading coverage values.
Reading maf file. 4476 mutations in 204 samples.
67 genes to display...
 q-values:
    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
0.00e+00 3.00e-08 2.70e-03 2.00e-02 4.15e-02 9.10e-02 
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 
