Man pages for GreenwoodLab/RVPedigree
Methods for Family-Based Rare-Variant Genetic Association Tests

ASKAT.regionRun the ASKAT method on a genomic region defined by a start...
compute.weightsCompute/create matrix with genotype weights
Estim.H0.ASKATEstimation of the variance components under the null model...
Estim.H0.NormalizedASKATEstimation of the variance components under the null model...
Estim.H0.VCCEstimate the model parameters under the null model
Get.GCreate genotypes from haplotypes
GetRelMatrixEstimate relationship matrix based on pedigree or genomic...
Normality.testTest for normality of the trait/phenotype
NormalizedASKAT.regionRun the normalized ASKAT method on a genomic region defined...
perm.hapPermute haplotypes
Preparation.hap.permPrepare for the haplotype permutation
Preparation.VCCPrepare for the VC-C methods
pvalue.ASKATCompute p-value and score for the ASKAT method
pvalue.NormalizedASKATCompute p-value and score for the normalized ASKAT method
pvalue.VCC1Compute score and p-value for the VC-C1 method
pvalue.VCC2Compute the p-value for the VC-C2 method
pvalue.VCC3Compute p-values for the VC-C3 method
read.haploRead haplotype data, selected by region of interest, from...
read.haplo.bedfileRead haplotype data, selected by region of interest, from BED...
read.haplo.pedfileRead haplotype data, selected by region of interest, from PED...
read.haplo.shapeit_hapsRead haplotype data, selected by region of interest, from a...
readMapFileRead file with information about SNPs chromosome and...
read.pedigreeRead pedigree structure from a Plink file
RVPedigreeRVPedigree main function
RVPedigree-packageRVPedigree: A package for region-based genetic association...
VCC1.regionRun the VC-C1 method on a genomic region defined by a start...
VCC2.regionRun the VC-C2 method on a genomic region defined by a start...
VCC3.regionRun the VC-C3 method on a genomic region defined by a start...
GreenwoodLab/RVPedigree documentation built on May 8, 2017, 12:57 p.m.