| cnv2cluster1 sample gene table file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/KICH-TP/3471877/all_lesions.conf_99.txt |
| Correlate_Clinical_Cnvs_onlysig2 clinical info file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KICH-TP/3351134/KICH-TP.clin.merged.picked.txt |
| Correlate_Clinical_Cnvs_onlysig2 filter cluster smaller than | 3 |
| Correlate_Clinical_Cnvs_onlysig2 output name | KICH-TP |
| Correlate_Clinical_Cnvs_onlysig2 figure height | 5 |
| Correlate_Clinical_Cnvs_onlysig2 figure width | 9 |
| Correlate_Clinical_Cnvs_onlysig2 survival legend position | OUT |
| Correlate_Clinical_Cnvs_onlysig2 pvalue cutoff | 1 |
| Correlate_Clinical_Cnvs_onlysig2 qvalue cutoff | 0.25 |
| Correlate_Clinical_Cnvs_onlysig2 make figure | ONLYSIG |
| Correlate_Clinical_Cnvs_onlysig2 nozzle ver | Nozzle.R1 |
| Execution Times: | |
| Submitted: | 11:23:13 06-06-13 |
| Completed: | |
| Elapsed: | 00 hrs 00 mins 39 secs |
step 1. cnv2cluster [id: 416912] Convert mutsig results to cluster files
urn:lsid:broadinstitute.org:cancer.genome.analysis:00494:12
| sample gene table file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/KICH-TP/3471877/all_lesions.conf_99.txt |
| maf file | |
| sig gene file | |
| sig gene q cutoff | 0.01 |
| output name |
| Output Files: | |
| all_lesions.conf_99.cnv.cluster.txt | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 11:23:16 06-06-13 |
| Completed: | 11:23:35 06-06-13 |
| Elapsed: | 00 hrs 00 mins 18 secs |
step 2. Correlate_Clinical_Cnvs_onlysig [id: 416913]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00495:49
| cluster label file | all_lesions.conf_99.cnv.cluster.txt |
| clinical info file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KICH-TP/3351134/KICH-TP.clin.merged.picked.txt |
| features used | ALL |
| filter cluster smaller than | 3 |
| output name | KICH-TP |
| 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 |
| Output Files: | |
| test_dim_tbl.txt | |
| nozzle.RData | |
| table.1.txt | |
| nozzle.html | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 11:23:16 06-06-13 |
| Completed: | 11:23:52 06-06-13 |
| Elapsed: | 00 hrs 00 mins 35 secs |