usage: spower LNR [-h] [-a MULTIPLIER] [-b MULTIPLIER] [-A MULTIPLIER]
[-B MULTIPLIER] [-c MULTIPLIER] [-d MULTIPLIER]
[--def_rare P] [--def_neutral VALUE VALUE]
[--def_protective VALUE VALUE] [-P P] [-Q P]
[--sample_size N] [--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 MULTIPLIER, --meanshift_rare_detrimental MULTIPLIER
mean shift in quantitative value w.r.t standard
deviation due to detrimental rare variants i.e., by
"MULTIPLIER * sigma" (default set to 0.0)
-b MULTIPLIER, --meanshift_rare_protective MULTIPLIER
mean shift in quantitative value w.r.t. standard
deviation due to protective rare variants i.e., by
"MULTIPLIER * sigma" (default set to 0.0)
-A MULTIPLIER, --meanshiftmax_rare_detrimental MULTIPLIER
maximum mean shift in quantitative value w.r.t
standard deviation due to detrimental rare variants
i.e., by "MULTIPLIER * sigma", applicable to variable
effects model (default set to None)
-B MULTIPLIER, --meanshiftmax_rare_protective MULTIPLIER
maximum mean shift in quantitative value w.r.t
standard deviation due to protective rare variants
i.e., by "MULTIPLIER * sigma", applicable to variable
effects model (default set to None)
-c MULTIPLIER, --meanshift_common_detrimental MULTIPLIER
mean shift in quantitative value w.r.t standard
deviation due to detrimental common variants i.e., by
"MULTIPLIER * sigma" (default set to 0.0)
-d MULTIPLIER, --meanshift_common_protective MULTIPLIER
mean shift in quantitative value w.r.t standard
deviation due to protective common variants i.e., by
"MULTIPLIER * sigma" (default set to 0.0)
--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 available)
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
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.