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| + | ===== Documentation ===== | ||
| + | ==== Data Input and Output ==== | ||
| + | * SEQPower [[http://bioinformatics.org/spower/input|input]] data | ||
| + | * SEQPower simulation of [[http://bioinformatics.org/spower/write|association data]] | ||
| + | * SEQPower power analysis [[http://bioinformatics.org/spower/output|results]] | ||
| + | * [[http://bioinformatics.org/spower/benchmark#usage|Graphic representation]] of power calculation results | ||
| + | |||
| + | ==== Complete List of Command Options ==== | ||
| + | [[http://bioinformatics.org/spower/allargs|Argument list]] | ||
| + | |||
| + | ==== Guide to Command Usage ==== | ||
| + | === Common options === | ||
| + | * Genotype simulation options | ||
| + | * Phenotype simulation options | ||
| + | * Analysis options | ||
| + | * Association tests options | ||
| + | * <color blue>Read more</color> [[http://bioinformatics.org/spower/options|>>]] | ||
| + | |||
| + | === Model specific options === | ||
| + | * [[http://bioinformatics.org/spower/mlogit|LOGIT]] model | ||
| + | * [[http://bioinformatics.org/spower/mpar|PAR]] model | ||
| + | * [[http://bioinformatics.org/spower/mlnr|LNR]] model | ||
| + | * [[http://bioinformatics.org/spower/melnr|ELNR]] model | ||
| + | * [[http://bioinformatics.org/spower/mblnr|BLNR]] model | ||
| + | |||
| + | ==== Genetic Sequences ==== | ||
| + | * Population genetics model based simulation | ||
| + | * ''spower simulate'' command for forward time simulation of DNA sequences | ||
| + | * Data based simulation | ||
| + | * Direct sampling from real world data-set | ||
| + | * <color blue>Read more</color> [[http://bioinformatics.org/spower/simseq|>>]] | ||
| + | |||
| + | ==== Disease Associations ==== | ||
| + | === Effects of variants === | ||
| + | * Fixed effect vs. variable effects | ||
| + | * Protective, deleterious and neutral variants | ||
| + | * <color blue>Read more</color> [[http://bioinformatics.org/spower/simtraits|>>]] | ||
| + | |||
| + | === Phenotype simulations === | ||
| + | * Linear mean-shift model | ||
| + | * Extreme quantitative trait model | ||
| + | * Logit model of odds ratios | ||
| + | * Population attributable risk model | ||
| + | * Linear model with qualitative outcome | ||
| + | * Phenotype simulation for sequences drawn from haplotype pools | ||
| + | * <color blue>Read more</color> [[http://bioinformatics.org/spower/simtraits|>>]] | ||
| + | |||
| + | ==== Power of Association Tests ==== | ||
| + | * [[http://bioinformatics.org/spower/cc|Analytic power and sample size calculation for case control design]] | ||
| + | * [[http://bioinformatics.org/spower/qt|Analytic power and sample size calculation for quantitative traits design]] | ||
| + | * [[http://bioinformatics.org/spower/empirical|Empirical power and sample size calculations]] | ||
| + | |||
| + | ==== Rare Variants Association Methods (RVAM) ==== | ||
| + | * [[http://bioinformatics.org/spower/vat-methods|RVAM]] catalog | ||
| + | * [[http://bioinformatics.org/spower/benchmark|Power comparison for RVAM]] | ||
| + | |||
| + | ==== Evaluating Novel Statistical Tests ==== | ||
| + | * Writing [[http://bioinformatics.org/spower/vat-r|R extensions]] | ||
