| cnvarms2cluster1 sample gene table file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/SKCM-NRAS_Hotspot_Mutants/3155578/broad_values_by_arm.txt |
| Correlate_Cluster_cnvarms_onlysig2 clinical info file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/SKCM-NRAS_Hotspot_Mutants/3157510/1.GDAC_mergedClustering.Finished/SKCM-NRAS_Hotspot_Mutants.transferedmergedcluster.txt |
| Correlate_Cluster_cnvarms_onlysig2 filter cluster smaller than | 3 |
| Correlate_Cluster_cnvarms_onlysig2 output name | SKCM-NRAS_Hotspot_Mutants |
| Correlate_Cluster_cnvarms_onlysig2 figure height | 5 |
| Correlate_Cluster_cnvarms_onlysig2 figure width | 9 |
| Correlate_Cluster_cnvarms_onlysig2 survival legend position | OUT |
| Correlate_Cluster_cnvarms_onlysig2 pvalue cutoff | 1 |
| Correlate_Cluster_cnvarms_onlysig2 qvalue cutoff | 0.25 |
| Correlate_Cluster_cnvarms_onlysig2 make figure | ONLYSIG |
| Correlate_Cluster_cnvarms_onlysig2 nozzle ver | Nozzle.R1 |
| Execution Times: | |
| Submitted: | 16:49:20 03-05-13 |
| Completed: | |
| Elapsed: | 00 hrs 01 mins 51 secs |
step 1. cnvarms2cluster [id: 399194] Convert mutsig results to cluster files
urn:lsid:broadinstitute.org:cancer.genome.analysis:00499:3
| sample gene table file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/SKCM-NRAS_Hotspot_Mutants/3155578/broad_values_by_arm.txt |
| maf file | |
| sig gene file | |
| sig gene q cutoff | 0.01 |
| output name |
| Output Files: | |
| broad_values_by_arm.mutsig.cluster.txt | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 16:49:23 03-05-13 |
| Completed: | 16:49:59 03-05-13 |
| Elapsed: | 00 hrs 00 mins 36 secs |
step 2. Correlate_Cluster_cnvarms_onlysig [id: 399195]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00508:2
| cluster label file | broad_values_by_arm.mutsig.cluster.txt |
| clinical info file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergedClusteringPipeline/SKCM-NRAS_Hotspot_Mutants/3157510/1.GDAC_mergedClustering.Finished/SKCM-NRAS_Hotspot_Mutants.transferedmergedcluster.txt |
| features used | ALL |
| filter cluster smaller than | 3 |
| output name | SKCM-NRAS_Hotspot_Mutants |
| figure height | 5 |
| figure width | 9 |
| survival legend position | OUT |
| pvalue cutoff | 1 |
| qvalue cutoff | 0.25 |
| make figure | ONLYSIG |
| nozzle ver | Nozzle.R1 |
| options | MUTSIG |
| report title | |
| job description |
| Execution Times: | |
| Submitted: | 16:49:23 03-05-13 |
| Completed: | 16:51:09 03-05-13 |
| Elapsed: | 00 hrs 01 mins 46 secs |