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| + | ===== SEQPower Benchmark ===== | ||
| + | ''spower execute'' command executes a given configuration file with parameters set to allow for power analysis under multiple scenarios within a single command. The feature also provides us a shortcut to benchmark performance of different rare variant association methods under various parameter settings. | ||
| + | ==== Prepare a Configuration File ==== | ||
| + | <hidden initialState="visible" -noprint> | ||
| + | <code text spower_benchmark.conf> | ||
| + | [model] | ||
| + | model=LOGIT;LOGIT,PAR,LNR | ||
| + | type=power | ||
| + | [input and output] | ||
| + | title=boyko1 | ||
| + | input=boyko1.gdat | ||
| + | resampling=False | ||
| + | output=PowerBenchmark | ||
| + | [runtime options] | ||
| + | verbosity=2 | ||
| + | seed=0 | ||
| + | jobs=8 | ||
| + | [sample population] | ||
| + | sample_size=2000;600,1000,2000,5000,10000 | ||
| + | p1=0.5;0.1,0.3,0.5,0.7,0.9 | ||
| + | [power calculation] | ||
| + | power=0.8 | ||
| + | replicates=1000 | ||
| + | alpha=0.05 | ||
| + | methods="CFisher --name CMC" "KBAC -p 2000 --adaptive 0.1" "WSSRankTest -p 2000 --adaptive 0.1 --name WSS" | ||
| + | [genotyping artifact] | ||
| + | missing_low_maf=None | ||
| + | missing_sites=None;0.05,0.2,0.4,0.6,0.8 | ||
| + | missing_sites_deleterious=None;0.05,0.2,0.4,0.6,0.8 | ||
| + | missing_sites_protective=None;0.05,0.2,0.4,0.6,0.8 | ||
| + | missing_sites_neutral=None;0.05,0.2,0.4,0.6,0.8 | ||
| + | missing_sites_synonymous=None;0.05,0.2,0.4,0.6,0.8 | ||
| + | missing_calls=None;0.05,0.2,0.4,0.6,0.8 | ||
| + | missing_calls_deleterious=None;0.05,0.2,0.4,0.6,0.8 | ||
| + | missing_calls_protective=None;0.05,0.2,0.4,0.6,0.8 | ||
| + | missing_calls_neutral=None;0.05,0.2,0.4,0.6,0.8 | ||
| + | missing_calls_synonymous=None;0.05,0.2,0.4,0.6,0.8 | ||
| + | error_calls=0.01 | ||
| + | error_calls_deleterious=None | ||
| + | error_calls_protective=None | ||
| + | error_calls_neutral=None | ||
| + | error_calls_synonymous=None | ||
| + | [quality control] | ||
| + | def_valid_locus=None | ||
| + | rare_only=False | ||
| + | missing_as_wt=True | ||
| + | discard_samples=None | ||
| + | discard_variants=None | ||
| + | [variants functionality] | ||
| + | def_rare=0.01 | ||
| + | def_neutral=-0.00001 0.00001 | ||
| + | def_protective=-1 -0.00001 | ||
| + | proportion_detrimental=None;None,0.8,0.6,0.4,0.2 | ||
| + | proportion_protective=None;0,0.25,0.5,0.75,None | ||
| + | [phenotype associations] | ||
| + | moi=A;A,D,R,M | ||
| + | OR_rare_detrimental=1.5;1.0,1.2,1.8,2.0,2.5,3.0 | ||
| + | OR_rare_protective=0.5;0.9,0.7,0.5,0.3,0.1 | ||
| + | ORmax_rare_detrimental=None;2.0,2.5,3.0,3.5,4.0 | ||
| + | ORmin_rare_protective=None;0.95,0.85,0.75,0.65,0.55 | ||
| + | OR_common_detrimental=1.0 | ||
| + | OR_common_protective=1.0 | ||
| + | baseline_effect=0.01 | ||
| + | PAR_rare_detrimental=0.0;0.005,0.01,0.015,0.025,0.05 | ||
| + | PAR_rare_protective=0.0 | ||
| + | PAR_common_detrimental=0.0 | ||
| + | PAR_common_protective=0.0 | ||
| + | PAR_variable=False | ||
| + | meanshift_rare_detrimental=0.5 | ||
| + | meanshift_rare_protective=-0.5 | ||
| + | meanshiftmax_rare_detrimental=None | ||
| + | meanshiftmax_rare_protective=None | ||
| + | meanshift_common_detrimental=0.0 | ||
| + | meanshift_common_protective=0.0 | ||
| + | QT_thresholds=0.5 0.5;0.1 0.9,0.2 0.8,0.3 0.7,0.4 0.6,0.5 0.5 | ||
| + | [plot] | ||
| + | x_axis=sample_size | ||
| + | x_axis_alias= | ||
| + | x_axis_fontsize= | ||
| + | y_axis=power | ||
| + | y_axis_range= | ||
| + | y_axis_fontsize= | ||
| + | stderr=power_std | ||
| + | object=method | ||
| + | object_alias= | ||
| + | object_color= | ||
| + | object_shape={{'CMC' : 1, 'BRV' : 3, 'WSS' : 5, 'KBAC' : 6, 'VT' : 7, 'c-alpha' : 10, 'RareCover' : 11, 'SKAT' : 15}} | ||
| + | object_line={{'CMC' : 1, 'BRV' : 6, 'WSS' : 1, 'KBAC' : 6, 'VT' : 1, 'c-alpha' : 6, 'RareCover' : 1, 'SKAT' : 6}} | ||
| + | plot_title= | ||
| + | plot_width= | ||
| + | plot_height= | ||
| + | plot_fn= | ||
| + | xlab= | ||
| + | xlab_fontsize= | ||
| + | ylab= | ||
| + | ylab_fontsize= | ||
| + | stderrlab= | ||
| + | objectlab= | ||
| + | condition= | ||
| + | </code> | ||
| + | </hidden>\\ | ||
| + | ==== Usage ==== | ||
| + | <code bash> | ||
| + | spower execute -h | ||
| + | </code>\\ | ||
| + | <hidden initialState="visible" -noprint> | ||
| + | usage: spower execute [-h] [-s [ARG [ARG ...]]] [-f [ARG [ARG ...]]] [--plot] | ||
| + | [--dry_run] | ||
| + | file | ||
| + | | ||
| + | positional arguments: | ||
| + | file configuration filename to execute | ||
| + | | ||
| + | optional arguments: | ||
| + | -h, --help show this help message and exit | ||
| + | -s [ARG [ARG ...]], --sliding [ARG [ARG ...]] | ||
| + | specify variable parameters | ||
| + | -f [ARG [ARG ...]], --fixed [ARG [ARG ...]] | ||
| + | specify fixed parameters | ||
| + | --plot generate plot instead of running simulations | ||
| + | --dry_run print generated commands to screen instead of | ||
| + | executing them | ||
| + | </hidden>\\ | ||
| + | === Execute benchmark === | ||
| + | <code bash> | ||
| + | spower execute spower-benchmark.conf --sliding sample_size=2000,3000,4000,5000,6000 \ | ||
| + | --fixed model=LOGIT input=KIT.gdat p1=0.5 | ||
| + | </code>\\ | ||
| + | <hidden initialState="visible" -noprint> | ||
| + | Running command 1/5 ... | ||
| + | INFO: Loading data from [KIT.gdat] ... | ||
| + | INFO: 1 units found | ||
| + | KIT : 100% |======================================================================================| Time: 0:03:06 | ||
| + | INFO: Tuning [PowerBenchmark.SEQPowerDB] ... | ||
| + | INFO: Result saved to [PowerBenchmark.csv/.loci.csv/.SEQPowerDB] | ||
| + | Running command 2/5 ... | ||
| + | INFO: Loading data from [KIT.gdat] ... | ||
| + | INFO: 1 units found | ||
| + | KIT : 100% |======================================================================================| Time: 0:05:08 | ||
| + | INFO: Tuning [PowerBenchmark.SEQPowerDB] ... | ||
| + | INFO: Result saved to [PowerBenchmark.csv/.loci.csv/.SEQPowerDB] | ||
| + | Running command 3/5 ... | ||
| + | INFO: Loading data from [KIT.gdat] ... | ||
| + | INFO: 1 units found | ||
| + | KIT : 100% |======================================================================================| Time: 0:07:32 | ||
| + | INFO: Tuning [PowerBenchmark.SEQPowerDB] ... | ||
| + | INFO: Result saved to [PowerBenchmark.csv/.loci.csv/.SEQPowerDB] | ||
| + | Running command 4/5 ... | ||
| + | INFO: Loading data from [KIT.gdat] ... | ||
| + | INFO: 1 units found | ||
| + | KIT : 100% |======================================================================================| Time: 0:10:06 | ||
| + | INFO: Tuning [PowerBenchmark.SEQPowerDB] ... | ||
| + | INFO: Result saved to [PowerBenchmark.csv/.loci.csv/.SEQPowerDB] | ||
| + | Running command 5/5 ... | ||
| + | INFO: Loading data from [KIT.gdat] ... | ||
| + | INFO: 1 units found | ||
| + | KIT : 100% |======================================================================================| Time: 0:14:09 | ||
| + | INFO: Tuning [PowerBenchmark.SEQPowerDB] ... | ||
| + | INFO: Result saved to [PowerBenchmark.csv/.loci.csv/.SEQPowerDB] | ||
| + | </hidden>\\ | ||
| + | === Generate plot === | ||
| + | <code bash> | ||
| + | spower execute spower-benchmark.conf --plot | ||
| + | </code>\\ | ||
| + | {{:plot-example.png?500.0}} | ||
