Examples¶

Following is an example of COMET usage and output on the command line:

$ hgmd input/ output/
Started on 2018-11-01T22:55:15.243954
Reading data...
Generating complement data...
########
# Processing cluster 1...
########
Running t test on singletons...
Running XL-mHG on singletons...
Creating discrete expression matrix...
Finding pair expression matrix...
Running hypergeometric test on pairs...
Finding simple true positives/negatives for singletons...
Finding simple true positives/negatives for pairs...
Pickling data for later...
Exporting cluster 1 output to CSV...
Drawing plots...
Drawing discrete plots...
Drawing combined plots...
Drawing singleton combined plots...
Drawing true positive/negative plots...
########
# Processing cluster 2...
########
Running t test on singletons...
Running XL-mHG on singletons...
Creating discrete expression matrix...
Finding pair expression matrix...
Running hypergeometric test on pairs...
Finding simple true positives/negatives for singletons...
Finding simple true positives/negatives for pairs...
Pickling data for later...
Exporting cluster 2 output to CSV...
Drawing plots...
Drawing discrete plots...
Drawing combined plots...
Drawing singleton combined plots...
Drawing true positive/negative plots...
########
# Processing cluster 3...
########
Running t test on singletons...
Running XL-mHG on singletons...
Creating discrete expression matrix...
Finding pair expression matrix...
Running hypergeometric test on pairs...
Finding simple true positives/negatives for singletons...
Finding simple true positives/negatives for pairs...
Pickling data for later...
Exporting cluster 3 output to CSV...
Drawing plots...
Drawing discrete plots...
Drawing combined plots...
Drawing singleton combined plots...
Drawing true positive/negative plots...
Ended on 2018-11-01T22:56:28.103160

Following are examples of COMET output:

pair_csv CSV output