| Interface | Description |
|---|---|
| AdditiveSite | |
| ForwardRegression |
| Class | Description |
|---|---|
| AbstractAdditiveSite |
This class holds data for a variant site to provide an object to hold data used and returned by a stepwise model fitter. That makes it convenient to use in a parallel stream for processing.
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| AbstractForwardRegression | |
| AddDomPermutationTestSpliterator |
This class calculates p-values for a test of a single SNP with a list of permuted data sets. myPermutedData is a list of double[] arrays, each of which is a data set to be tested. This class extends a parent class which tests an additive only model to test an additive + dominance model instead.
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| AddPlusDomModelEffect |
A ModelEffect that takes an AdditiveSite as an argument and uses the additiveCovariate from that object to compute a covariate representing dominance. In general, the AdditiveSite will be supplied as the id, although that is not a requirement. The dominance values are calculated as 1 - abs(x - 1) where x is the addivitive value. The values of x are expected to be 0, 1, 2, where 0 and 1 are homozygous genotypes and 1 is the het.
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| AdditiveModelForwardRegression | |
| AdditiveResidualForwardRegression | |
| AdditiveSiteStorePlugin | |
| CovariatePermutationTestSpliterator |
A Spliterator that uses the covariate from an AdditiveSite to test it against a baseModel and a list of permuted data sets using a fixed effect linear model. This class is used as part of stepwise model fitting to process a list of AdditiveSites. The permutation test is used to determine the entry and exit limits to be used for model fitting.
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| ForwardStepAddDomSpliterator | |
| ForwardStepAdditiveSpliterator |
This Spliterator is used to fit a baseModel plus an additive effect covariate to a data set y. It takes an AdditiveSite as input, calculates the test statistic specified by selectionCriterion, and sets its value in the AdditiveSite.
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| ForwardStepNestedAdditiveSpliterator | |
| ForwardStepSubsettingAdditiveSpliterator | |
| ForwardStepSubsettingNestedAdditiveSpliterator | |
| GenotypeAdditiveSite |
GenotypeAdditiveSite is an AdditiveSite that takes a byte[] array of genotypes as input and converts them to a double[] array. It codes the homozygous major as 2, homozygous minor as 0 and het as 1. It then subtracts the mean value from all elements of the array and sets missing to zero (now the mean). For efficient storage, the values of 0,1,2,3 are stored in a byte array which indexes the double values.
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| NestedCovariatePermutationTestSpliterator | |
| RefProbAdditiveSite |
An AdditiveSite that takes a float[] valued covariate as an argument. The covariate should equal the probability that a given allele (major or minor, for example) would be selected at random from that site. It also stores the value of a statistic determined by selectionCriteria which results from fitting a linear model.
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| ResamplingGWASPlugin | |
| SNP | |
| StepwiseAddDomModelFitter |
Fits an additive plus dominance model in a stepwise fashion. See StepwiseAdditiveModelFitter for a desription of outputs available.
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| StepwiseAdditiveModelFitter |
A multi-threaded stepwise model fitter for additive only models. To use it first construct an object then call runAnalysis(). After the analysis has run, any of several reports will be available using getters. If a permutation test is requested it is run first. The analysis then fits SNPs consecutively, then rescans the full model to determine if any of the SNPs has a better choice given all the other SNPs in the model. As part of the rescan it calculates a support interval for each of the SNPs. Reports available include the steps taken to fit the model with sequential p-values, an anova with marginal p-values, a report of marker effects, a post-scan anova, post-scan marker effects, and a permutation report. It will also output a list of model residuals by chromosome. For each chromosome, it reports the residuals from a model that includes all effects, except the markers on that chromosome.
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| StepwiseAdditiveModelFitterPlugin | |
| StepwiseOLSModelFitter | |
| StepwiseOLSModelFitterPlugin |
Stepwise Ordinary Least Squares model fitter
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