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