===== 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}}