User Tools


Differences

This shows you the differences between two versions of the page.

Link to this comparison view

allargs [2016/04/13 18:02]
allargs [2016/04/13 18:02] (current)
Line 1: Line 1:
 +~~NOTOC~~
 +
 +===== Table of Command Options =====
 +=== Common options ===
 +<WRAP center 105%>
 +^  Option ​ ^  Default ​ ^  Description ​ ^
 +|  %%--%%moi ​ |  A  |  mode of inheritance:​ '​A',​ additive ​ |
 +|  %%--%%resampling ​ |  False  |  directly draw sample genotypes from given haplotype pools (sample genotypes will be simulated on the fly if haplotype pools are not avaliable) ​ |
 +|  %%--%%def_rare ​ |  0.01  |  definition of rare variants: variant having 'MAF <= frequency'​ will be considered a '​rare'​ variant; the opposite set is considered '​common' ​ |
 +|  %%--%%def_neutral ​ |  None  |  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 ​ |
 +|  %%--%%def_protective ​ |  None  |  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 ​ |
 +|  -P/​%%--%%proportion_detrimental ​ |  None  |  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 ​ |
 +|  -Q/​%%--%%proportion_protective ​ |  None  |  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 ​ |
 +|  %%--%%sample_size ​ |  None  |  total sample size  |
 +|  %%--%%p1 ​ |  None  |  proportion of affected individuals , 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). ​ |
 +|  %%--%%def_valid_locus ​ |  None  |  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 ​ |
 +|  %%--%%rare_only ​ |  False  |  remove from analysis common variant sites in the population, i.e., those in the haplotype pool having MAF > $def_rare ​ |
 +|  %%--%%missing_as_wt ​ |  False  |  label missing genotype calls as wildtype genotypes ​ |
 +|  %%--%%missing_low_maf ​ |  None  |  variant sites having population MAF < P are set to missing ​ |
 +|  %%--%%missing_sites ​ |  None  |  proportion of missing variant sites  |
 +|  %%--%%missing_sites_deleterious ​ |  None  |  proportion of missing deleterious sites  |
 +|  %%--%%missing_sites_protective ​ |  None  |  proportion of missing protective sites  |
 +|  %%--%%missing_sites_neutral ​ |  None  |  proportion of missing neutral sites  |
 +|  %%--%%missing_sites_synonymous ​ |  None  |  proportion of missing synonymous sites  |
 +|  %%--%%missing_calls ​ |  None  |  proportion of missing genotype calls  |
 +|  %%--%%missing_calls_deleterious ​ |  None  |  proportion of missing genotype calls at deleterious sites  |
 +|  %%--%%missing_calls_protective ​ |  None  |  proportion of missing genotype calls at protective sites  |
 +|  %%--%%missing_calls_neutral ​ |  None  |  proportion of missing genotype calls at neutral sites  |
 +|  %%--%%missing_calls_synonymous ​ |  None  |  proportion of missing genotype calls at synonymous sites  |
 +|  %%--%%error_calls ​ |  None  |  proportion of error genotype calls  |
 +|  %%--%%error_calls_deleterious ​ |  None  |  proportion of error genotype calls at deleterious sites  |
 +|  %%--%%error_calls_protective ​ |  None  |  proportion of error genotype calls at protective sites  |
 +|  %%--%%error_calls_neutral ​ |  None  |  proportion of error genotype calls at neutral sites  |
 +|  %%--%%error_calls_synonymous ​ |  None  |  proportion of error genotype calls at synonymous sites  |
 +|  %%--%%power ​ |  None  |  power for which total sample size is calculated (this option is mutually exclusive with option '​%%--%% sample_size'​) ​ |
 +|  -r/​%%--%%replicates ​ |  1  |  number of replicates for power evaluation ​ |
 +|  %%--%%alpha ​ |  0.05  |  significance level at which power will be evaluated ​ |
 +|  -l/​%%--%%limit ​ |  None  |  if specified, will limit calculations to the first N groups in data .  |
 +|  -o/​%%--%%output ​ |  None  |  output filename ​ |
 +|  -t/​%%--%%title ​ |  None  |  unique identifier of a single command run  |
 +|  -v/​%%--%%verbosity ​ |  2  |  verbosity level: 0 for absolutely quiet, 1 for less verbose, 2 for verbose, 3 for more debug information ​ |
 +|  -s/​%%--%%seed ​ |  0  |  seed for random number generator, 0 for random seed  |
 +|  -j/​%%--%%jobs ​ |  2  |  number of CPUs to use when multiple replicates are required via '​-r'​ option .  |
 +|  -m/​%%--%%methods ​ |  None  |  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.  |
 +|  %%--%%discard_samples ​ |  None  |  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 ​ |  None  |  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. ​ |
 +</​WRAP>​
 +
 +=== LOGIT model options ===
 +<WRAP center 105%>
 +^  Option ​ ^  Default ​ ^  Description ​ ^
 +|  -a/​%%--%%OR_rare_detrimental ​ |  1.0  |  odds ratio for detrimental rare variants ​ |
 +|  -b/​%%--%%OR_rare_protective ​ |  1.0  |  odds ratio for protective rare variants ​ |
 +|  -A/​%%--%%ORmax_rare_detrimental ​ |  None  |  maximum odds ratio for detrimental rare variants, applicable to variable effects model  |
 +|  -B/​%%--%%ORmin_rare_protective ​ |  None  |  minimum odds ratio for protective rare variants, applicable to variable effects model  |
 +|  -c/​%%--%%OR_common_detrimental ​ |  1.0  |  odds ratio for detrimental common variants ​ |
 +|  -d/​%%--%%OR_common_protective ​ |  1.0  |  odds ratio for protective common variants ​ |
 +|  -f/​%%--%%baseline_effect ​ |  0.01  |  penetrance of wildtype genotypes ​ |
 +</​WRAP>​
 +
 +=== PAR model options ===
 +<WRAP center 105%>
 +^  Option ​ ^  Default ​ ^  Description ​ ^
 +|  -a/​%%--%%PAR_rare_detrimental ​ |  0.0  |  Population attributable risk for detrimental rare variants ​ |
 +|  -b/​%%--%%PAR_rare_protective ​ |  0.0  |  Population attributable risk for protective rare variants ​ |
 +|  -c/​%%--%%PAR_common_detrimental ​ |  0.0  |  Population attributable risk for detrimental common variants ​ |
 +|  -d/​%%--%%PAR_common_protective ​ |  0.0  |  Population attributable risk for protective common variants ​ |
 +|  %%--%%PAR_variable ​ |  False  |  use variable population attributable risks: the smaller the MAF the larger the PAR  |
 +|  -f/​%%--%%baseline_effect ​ |  0.01  |  penetrance of wildtype genotypes ​ |
 +</​WRAP>​
 +
 +=== LNR model options ===
 +<WRAP center 105%>
 +^  Option ​ ^  Default ​ ^  Description ​ ^
 +|  -a/​%%--%%meanshift_rare_detrimental ​ |  0.0  |  mean shift in quantitative value w.r.t standard deviation due to detrimental rare variants i.e., by '​MULTIPLIER * sigma' ​ |
 +|  -b/​%%--%%meanshift_rare_protective ​ |  0.0  |  mean shift in quantitative value w.r.t. standard deviation due to protective rare variants i.e., by '​MULTIPLIER * sigma' ​ |
 +|  -A/​%%--%%meanshiftmax_rare_detrimental ​ |  None  |  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  |
 +|  -B/​%%--%%meanshiftmax_rare_protective ​ |  None  |  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  |
 +|  -c/​%%--%%meanshift_common_detrimental ​ |  0.0  |  mean shift in quantitative value w.r.t standard deviation due to detrimental common variants i.e., by '​MULTIPLIER * sigma' ​ |
 +|  -d/​%%--%%meanshift_common_protective ​ |  0.0  |  mean shift in quantitative value w.r.t standard deviation due to protective common variants i.e., by '​MULTIPLIER * sigma' ​ |
 +</​WRAP>​
 +
 +=== BLNR & ELNR model options ===
 +<WRAP center 105%>
 +^  Option ​ ^  Default ​ ^  Description ​ ^
 +|  -a/​%%--%%meanshift_rare_detrimental ​ |  0.0  |  mean shift in quantitative value w.r.t standard deviation due to detrimental rare variants i.e., by '​MULTIPLIER * sigma' ​ |
 +|  -b/​%%--%%meanshift_rare_protective ​ |  0.0  |  mean shift in quantitative value w.r.t. standard deviation due to protective rare variants i.e., by '​MULTIPLIER * sigma' ​ |
 +|  -A/​%%--%%meanshiftmax_rare_detrimental ​ |  None  |  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  |
 +|  -B/​%%--%%meanshiftmax_rare_protective ​ |  None  |  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  |
 +|  -c/​%%--%%meanshift_common_detrimental ​ |  0.0  |  mean shift in quantitative value w.r.t standard deviation due to detrimental common variants i.e., by '​MULTIPLIER * sigma' ​ |
 +|  -d/​%%--%%meanshift_common_protective ​ |  0.0  |  mean shift in quantitative value w.r.t standard deviation due to protective common variants i.e., by '​MULTIPLIER * sigma' ​ |
 +|  %%--%%QT_thresholds ​ |  [0.5, 0.5]  |  lower/​uppwer percentile cutoffs for quantitative traits in extreme QT sampling ​ |
 +</​WRAP>​
 +
 +=== show command option ===
 +<WRAP center 105%>
 +^  Option ​ ^  Default ​ ^  Description ​ ^
 +|  <​args> ​ |  None  |  type of information to display, which can be '​tests'​ for a list of all association tests, 'test TST' for details of an association test TST, '​FILENAME.csv'​ for all column names in a csv file, '​FILENAME.csv [colnames]'​ for values of columns in a csv file; '​FILENAME.SEQPowerDB'​ for all table names in a SEQPower database file, '​FILENAME.SEQPowerDB TABLE' for all column names in a table, '​FILENAME.SEQPowerDB TABLE [colnames]'​ for values of specified columns in a table, and '​FILENAME.SEQPowerDB TABLE [colnames] %%--%%condition QUERY' for filtered/​formatted values of columns in a table. Wildcard symbol '​*'​ for colnames is allowed. ​ |
 +|  %%--%%border ​ |  full  |  table border ​ |
 +</​WRAP>​
 +
 +=== execute command option ===
 +<WRAP center 105%>
 +^  Option ​ ^  Default ​ ^  Description ​ ^
 +|  -s/​%%--%%sliding ​ |  None  |  specify variable parameters ​ |
 +|  -f/​%%--%%fixed ​ |  None  |  specify fixed parameters ​ |
 +|  %%--%%plot ​ |  False  |  generate plot instead of running simulations ​ |
 +|  %%--%%dry_run ​ |  False  |  print generated commands to screen instead of executing them  |
 +</​WRAP>​