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--- mblnr [2016/04/13 18:02]
+++ mblnr [2016/04/13 18:02] (current)
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+===== Linear Model Binary Outcome =====
+Under this model, case control status are simulated based on QT values. Quantitative traits are generated; Cases are defined as samples having QT values larger than \(p^{th}\) upper percentile, and controls are samples having QT values smaller than \(q^{th}\) lower percentile. Since under this model MAF for case or ctrl groups are mathematically intractable, only empirical power and sample size analysis are applicable.
+==== Command Interface ====
+<code bash>
+spower BLNR -h
+</code>\\
+<hidden initialState="visible" -noprint>
+  usage: spower BLNR [-h] [-a MULTIPLIER] [-b MULTIPLIER] [-A MULTIPLIER]
+                     [-B MULTIPLIER] [-c MULTIPLIER] [-d MULTIPLIER]
+                     [--QT_thresholds C C] [--sample_size N] [--p1 P]
+                     [--def_rare P] [--def_neutral VALUE VALUE]
+                     [--def_protective VALUE VALUE] [-P P] [-Q 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 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)
+    --QT_thresholds C C   lower/uppwer percentile cutoffs for quantitative
+                          traits in extreme QT sampling, default to "0.5 0.5"
+    --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)
+  sample population:
+    --sample_size N       total sample size
+    --p1 P                proportion of affected individuals (default set to
+.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).
+  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
+.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)
+  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
+" "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.
+</hidden>\\
+==== Details ====
+Model specific options are similar to options in [[http://bioinformatics.org/spower/lnr|''LNR'']] model. General simulation and analysis options are [[http://bioinformatics.org/spower/options|otherwise documented]]. The infinite sample pool method is triggered by ''%%--%%p1'' option. If ''%%--%%p1'' is not specified, the finite sample pool method will be used.
+=== --QT_thresholds ===
+This option takes two values, the lower and upper QT percentile cutoff which defines case control status. QT values under the lower cutoff are considered controls; QT values higher than the upper cutoff are considered cases.
+==== Examples ====
+	*  [[http://bioinformatics.org/spower/empirical-tutorial|Empirical power analysis]] for case control studies

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