def run_experiment(self, params, experiment, plink_path, power_file, with_cov):
postfix = "with_cov"
if not with_cov:
postfix = "without_cov"
for model_id, model in enumerate( experiment[ 'models' ] ):
covariates = model[ 'covariates' ]
if not with_cov:
covariates = None
params = updated_params( params, model )
self.method_handler.start_experiment( experiment[ 'name' ], model_id, postfix )
for i in range( params.num_pairs ):
plinkdata.generate_sufficient_cov_data( params,
model[ 'params' ],
covariates,
plink_path )
program.run_methods( params, plink_path, self.method_handler, with_cov )
xvalue = model.get( 'xvalue', None )
if not xvalue:
xvalue = model_id
self.method_handler.reset_files( )
method_power = program.calculate_power( params, self.method_handler )
for method_name, power_data in method_power.iteritems( ):
power, lower, upper = power_data
line = "{0}\t{1}\t{2}\t{3}\t{4}\t{5}\n".format( method_name, xvalue, power, lower, upper, int( with_cov ) )
power_file.write( line )
def calculate_power(self, params, experiment, plink_path, power_file):
ld = experiment.get( "ld", 0.0 )
for model_id, model in enumerate( experiment[ 'models' ] ):
params = updated_params( params, model )
plinkdata.generate_data( params,
model[ 'params' ],
ld, plink_path )
self.method_handler.start_experiment( experiment[ 'name' ], model_id )
program.run_methods( params, plink_path, self.method_handler )
self.method_handler.reset_files( )
xvalue = model.get( 'xvalue', None )
if not xvalue:
xvalue = model_id
method_power = program.calculate_power( params, self.method_handler )
for method_name, power_data in method_power.iteritems( ):
power, lower, upper = power_data
line = "{0}\t{1}\t{2}\t{3}\t{4}\n".format( method_name, xvalue, power, lower, upper )
power_file.write( line )