Methods for Family-Based Rare-Variant Genetic Association Tests


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Documentation for package ‘RVPedigree’ version 0.0.3

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RVPedigree-package RVPedigree: A package for region-based genetic association tests.
ASKAT.region Run the ASKAT method on a genomic region defined by a start and a stop base pair coordinate
Estim.H0.ASKAT Estimation of the variance components under the null model using the ASKAT method
Estim.H0.NormalizedASKAT Estimation of the variance components under the null model using the normalized ASKAT method
Estim.H0.VCC Estimate the model parameters under the null model
GetRelMatrix Estimate relationship matrix based on pedigree or genomic data
Normality.test Test for normality of the trait/phenotype
NormalizedASKAT.region Run the normalized ASKAT method on a genomic region defined by a start and a stop base pair coordinate
readMapFile Read file with information about SNPs chromosome and position, for example from regular PLINK .map OR .bim file
RVPedigree RVPedigree main function
VCC1.region Run the VC-C1 method on a genomic region defined by a start and a stop base pair coordinate
VCC2.region Run the VC-C2 method on a genomic region defined by a start and a stop base pair coordinate
VCC3.region Run the VC-C3 method on a genomic region defined by a start and a stop base pair coordinate