usage: spower LOGIT [-h] [-a GAMMA] [-b GAMMA] [-A GAMMA] [-B GAMMA]
[-c GAMMA] [-d GAMMA] [-f P] [--def_rare P]
[--def_neutral VALUE VALUE] [--def_protective VALUE VALUE]
[-P P] [-Q P] [--sample_size N] [--p1 P]
[--def_valid_locus VALUE VALUE] [--rare_only]
[--missing_as_wt] [--missing_low_maf P]
[--missing_sites P] [--missing_sites_deleterious P]
[--missing_sites_protective P] [--missing_sites_neutral P]
[--missing_sites_synonymous P] [--missing_calls P]
[--missing_calls_deleterious P]
[--missing_calls_protective P] [--missing_calls_neutral P]
[--missing_calls_synonymous P] [--error_calls P]
[--error_calls_deleterious P] [--error_calls_protective P]
[--error_calls_neutral P] [--error_calls_synonymous P]
[--power P] [-r N] [--alpha ALPHA] [--moi {A,D,R,M}]
[--resampling] [-l N] [-o file] [-t NAME] [-v {0,1,2,3}]
[-s N] [-j N] [-m METHODS [METHODS ...]]
[--discard_samples [EXPR [EXPR ...]]]
[--discard_variants [EXPR [EXPR ...]]]
DATA
positional arguments:
DATA name of input data or prefix of input data bundle (see
the documentation for details)
optional arguments:
-h, --help show this help message and exit
model parameters:
-a GAMMA, --OR_rare_detrimental GAMMA
odds ratio for detrimental rare variants (default set
to 1.0)
-b GAMMA, --OR_rare_protective GAMMA
odds ratio for protective rare variants (default set
to 1.0)
-A GAMMA, --ORmax_rare_detrimental GAMMA
maximum odds ratio for detrimental rare variants,
applicable to variable effects model (default set to
None)
-B GAMMA, --ORmin_rare_protective GAMMA
minimum odds ratio for protective rare variants,
applicable to variable effects model (default set to
None)
-c GAMMA, --OR_common_detrimental GAMMA
odds ratio for detrimental common variants (default
set to 1.0)
-d GAMMA, --OR_common_protective GAMMA
odds ratio for protective common variants (default set
to 1.0)
-f P, --baseline_effect P
penetrance of wildtype genotypes (default set to 0.01)
--moi {A,D,R,M} mode of inheritance: "A", additive (default); "D",
dominant; "R", recessive; "M", multiplicative (does
not apply to quantitative traits model)
--resampling directly draw sample genotypes from given haplotype
pools (sample genotypes will be simulated on the fly
if haplotype pools are not avaliable)
variants functionality:
--def_rare P definition of rare variants: variant having "MAF <=
frequency" will be considered a "rare" variant; the
opposite set is considered "common" (default set to
0.01)
--def_neutral VALUE VALUE
annotation value cut-offs that defines a variant to be
"neutral" (e.g. synonymous, non-coding etc. that will
not contribute to any phenotype); any variant with
"function_score" X falling in this range will be
considered neutral (default set to None)
--def_protective VALUE VALUE
annotation value cut-offs that defines a variant to be
"protective" (i.e., decrease disease risk or decrease
quantitative traits value); any variant with
"function_score" X falling in this range will be
considered protective (default set to None)
-P P, --proportion_detrimental P
proportion of deleterious variants associated with the
trait of interest, i.e., the random set of the rest (1
- p) x 100% deleterious variants are non-causal: they
do not contribute to the phenotype in simulations yet
will present as noise in analysis (default set to
None)
-Q P, --proportion_protective P
proportion of protective variants associated with the
trait of interest, i.e., the random set of the rest (1
- p) x 100% protective variants are non-causal: they
do not contribute to the phenotype in simulations yet
will present as noise in analysis (default set to
None)
sample population:
--sample_size N total sample size
--p1 P proportion of affected individuals (default set to
0.5), or individuals with high extreme QT values
sampled from infinite population (default set to None,
meaning to sample from finite population speficied by
--sample_size option).
quality control:
--def_valid_locus VALUE VALUE
upper and lower bounds of variant counts that defines
if a locus is "valid", i.e., locus having number of
variants falling out of this range will be ignored
from power calculation (default set to None)
--rare_only remove from analysis common variant sites in the
population, i.e., those in the haplotype pool having
MAF > $def_rare
--missing_as_wt label missing genotype calls as wildtype genotypes
sequencing / genotyping artifact:
--missing_low_maf P variant sites having population MAF < P are set to
missing
--missing_sites P proportion of missing variant sites
--missing_sites_deleterious P
proportion of missing deleterious sites
--missing_sites_protective P
proportion of missing protective sites
--missing_sites_neutral P
proportion of missing neutral sites
--missing_sites_synonymous P
proportion of missing synonymous sites
--missing_calls P proportion of missing genotype calls
--missing_calls_deleterious P
proportion of missing genotype calls at deleterious
sites
--missing_calls_protective P
proportion of missing genotype calls at protective
sites
--missing_calls_neutral P
proportion of missing genotype calls at neutral sites
--missing_calls_synonymous P
proportion of missing genotype calls at synonymous
sites
--error_calls P proportion of error genotype calls
--error_calls_deleterious P
proportion of error genotype calls at deleterious
sites
--error_calls_protective P
proportion of error genotype calls at protective sites
--error_calls_neutral P
proportion of error genotype calls at neutral sites
--error_calls_synonymous P
proportion of error genotype calls at synonymous sites
power calculation:
--power P power for which total sample size is calculated (this
option is mutually exclusive with option '--
sample_size')
-r N, --replicates N number of replicates for power evaluation (default set
to 1)
--alpha ALPHA significance level at which power will be evaluated
(default set to 0.05)
input/output specifications:
-l N, --limit N if specified, will limit calculations to the first N
groups in data (default set to None)
-o file, --output file
output filename
runtime options:
-t NAME, --title NAME
unique identifier of a single command run (default to
output filename prefix)
-v {0,1,2,3}, --verbosity {0,1,2,3}
verbosity level: 0 for absolutely quiet, 1 for less
verbose, 2 for verbose, 3 for more debug information
(default set to 2)
-s N, --seed N seed for random number generator, 0 for random seed
(default set to 0)
-j N, --jobs N number of CPUs to use when multiple replicates are
required via "-r" option (default set to 2)
association tests:
-m METHODS [METHODS ...], --methods METHODS [METHODS ...]
Method of one or more association tests. Parameters
for each method should be specified together as a
quoted long argument (e.g. --methods "m --alternative
2" "m1 --permute 1000"), although the common method
parameters can be specified separately, as long as
they do not conflict with command arguments. (e.g.
--methods m1 m2 -p 1000 is equivalent to --methods "m1
-p 1000" "m2 -p 1000".). You can use command 'spower
show tests' for a list of association tests, and
'spower show test TST' for details about a test.
samples and genotypes filtering:
--discard_samples [EXPR [EXPR ...]]
Discard samples that match specified conditions within
each test group. Currently only expressions in the
form of "%(NA)>p" is provided to remove samples that
have more 100*p percent of missing values.
--discard_variants [EXPR [EXPR ...]]
Discard variant sites based on specified conditions
within each test group. Currently only expressions in
the form of '%(NA)>p' is provided to remove variant
sites that have more than 100*p percent of missing
genotypes. Note that this filter will be applied after
"--discard_samples" is applied, if the latter also is
specified.
