| Usage: gdac_counts [flags] <directory> | <file> ... <file> |
| Version: 0.5.5 |
| Parse Broad GDAC samplestamp files to summarize the data contained |
| within, by counting per tumor which data types have how many sample |
| counts. |
| Specify either a directory (or tree) containing multiple samplestamp |
| files, which represent normed data from DCC, or a list of one or more |
| samplestamp files. |
| Flags: |
| -cohort <string> show counts/samples for the single named disease cohort |
| -html generate HTML version of counts table |
| -list display the samples, instead of counting, per datatype |
| (also displays Firehose platform annotations for each) |
| -png generate png version of counts table |
| -prefix <string> prefix to use for HTML and PNG files (default: gdac_counts) |
| -totals output a row showing the totals for each column |
| -what display what is being counted, and how |
| Examples: |
| % gdac_counts `gdac_data -s` |
| Show counts for the samplestamps of the latest dicing |
| % gdac_counts -list -cohort STAD `gdac_data -s` |
| Display list of sample aliquots, again in latest dicing, but only STAD |
| % cd /xchip/gdac_data/normalized/loadfiles/prod/prod__2011_07_28 |
| % gdac_counts . |