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docs [2016/04/13 18:02]
docs [2016/04/13 18:02] (current)
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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]]