RVPedigree: Methods for Family-Based Rare-Variant Genetic Association Tests

This is a collection of the five region-based rare-variant genetic association tests. The following tests are currently implemented: ASKAT, ASKAT-Normalized, VC-C1, VC-C2 and VC-C3.

AuthorKarim Oualkacha [aut, cre], M'Hamed Lajmi Lakhal-Chaieb [aut], Celia M.T. Greenwood [aut], Lennart C. Karssen [aut], Sodbo Sharapov [aut]
Date of publication2016-01-20 09:12:22
MaintainerKarim Oualkacha <oualkacha.karim@uqam.ca>
LicenseGPL (>= 3)
Version0.0.3

View on CRAN

Man pages

ASKAT.region: Run the ASKAT method on a genomic region defined by a start...

compute.weights: Compute/create matrix with genotype weights

Estim.H0.ASKAT: Estimation of the variance components under the null model...

Estim.H0.NormalizedASKAT: Estimation of the variance components under the null model...

Estim.H0.VCC: Estimate the model parameters under the null model

Get.G: Create genotypes from haplotypes

GetRelMatrix: Estimate relationship matrix based on pedigree or genomic...

Normality.test: Test for normality of the trait/phenotype

NormalizedASKAT.region: Run the normalized ASKAT method on a genomic region defined...

perm.hap: Permute haplotypes

Preparation.hap.perm: Prepare for the haplotype permutation

Preparation.VCC: Prepare for the VC-C methods

pvalue.ASKAT: Compute p-value and score for the ASKAT method

pvalue.NormalizedASKAT: Compute p-value and score for the normalized ASKAT method

pvalue.VCC1: Compute score and p-value for the VC-C1 method

pvalue.VCC2: Compute the p-value for the VC-C2 method

pvalue.VCC3: Compute p-values for the VC-C3 method

read.haplo: Read haplotype data, selected by region of interest, from...

read.haplo.bedfile: Read haplotype data, selected by region of interest, from BED...

read.haplo.pedfile: Read haplotype data, selected by region of interest, from PED...

read.haplo.shapeit_haps: Read haplotype data, selected by region of interest, from a...

readMapFile: Read file with information about SNPs chromosome and...

read.pedigree: Read pedigree structure from a Plink file

RVPedigree: RVPedigree main function

RVPedigree-package: RVPedigree: A package for region-based genetic association...

VCC1.region: Run the VC-C1 method on a genomic region defined by a start...

VCC2.region: Run the VC-C2 method on a genomic region defined by a start...

VCC3.region: Run the VC-C3 method on a genomic region defined by a start...

Files in this package

RVPedigree
RVPedigree/inst
RVPedigree/inst/CITATION
RVPedigree/inst/extdata
RVPedigree/inst/extdata/genes.lst
RVPedigree/inst/extdata/test.map
RVPedigree/inst/extdata/data_nullmorgans.map
RVPedigree/inst/extdata/dataT.tfam
RVPedigree/inst/extdata/data.map
RVPedigree/inst/extdata/test.bed
RVPedigree/inst/extdata/genes2.lst
RVPedigree/inst/extdata/covariates.dat
RVPedigree/inst/extdata/gwaa.data.RData
RVPedigree/inst/extdata/dataB.bed
RVPedigree/inst/extdata/pheno.dat
RVPedigree/inst/extdata/data.phe
RVPedigree/inst/extdata/NNormTrait.dat
RVPedigree/inst/extdata/data.ped
RVPedigree/inst/extdata/test.ped
RVPedigree/inst/extdata/test.bim
RVPedigree/inst/extdata/OneFamilyExample.ped
RVPedigree/inst/extdata/covariates2.dat
RVPedigree/inst/extdata/kinmat.Rdata
RVPedigree/inst/extdata/TwoFamilyExample.ped
RVPedigree/inst/extdata/test.fam
RVPedigree/inst/extdata/dataB.bim
RVPedigree/inst/extdata/dataT.tped
RVPedigree/inst/extdata/dataB.fam
RVPedigree/inst/doc
RVPedigree/inst/doc/vignette.Rnw
RVPedigree/inst/doc/vignette.pdf
RVPedigree/inst/doc/vignette.R
RVPedigree/NAMESPACE
RVPedigree/R
RVPedigree/R/read.haplo.R RVPedigree/R/VCC3.region.R RVPedigree/R/RVPedigree-package.R RVPedigree/R/pvalue.NormalizedASKAT.R RVPedigree/R/pvalue.VCC3.R RVPedigree/R/read.haplo.bedfile.R RVPedigree/R/pvalue.VCC1.R RVPedigree/R/VCC2.region.R RVPedigree/R/Neg.LogLikelihood.ASKAT.R RVPedigree/R/Estim.H0.VCC.R RVPedigree/R/read.pedigree.R RVPedigree/R/Normality.test.R RVPedigree/R/VCC1.region.R RVPedigree/R/Estim.H0.NormalizedASKAT.R RVPedigree/R/Get.G.R RVPedigree/R/Preparation.hap.perm.R RVPedigree/R/Neg.LogLikelihood.VC.C1.R RVPedigree/R/NormalizedASKAT.region.R RVPedigree/R/Preparation.VCC.R RVPedigree/R/ASKAT.region.R RVPedigree/R/read.haplo.shapeit-haps.R RVPedigree/R/inputChecks.R RVPedigree/R/pvalue.ASKAT.R RVPedigree/R/compute.weights.R RVPedigree/R/pvalue.VCC2.R RVPedigree/R/GetRelMatrix.R RVPedigree/R/Estim.H0.ASKAT.R RVPedigree/R/meiose.R RVPedigree/R/perm.hap.R RVPedigree/R/RVPedigree.R RVPedigree/R/findParentIndices.R RVPedigree/R/readMapFile.R RVPedigree/R/read.haplo.pedfile.R
RVPedigree/vignettes
RVPedigree/vignettes/vignette.Rnw
RVPedigree/MD5
RVPedigree/build
RVPedigree/build/vignette.rds
RVPedigree/DESCRIPTION
RVPedigree/man
RVPedigree/man/GetRelMatrix.Rd RVPedigree/man/pvalue.ASKAT.Rd RVPedigree/man/Normality.test.Rd RVPedigree/man/Preparation.VCC.Rd RVPedigree/man/read.haplo.pedfile.Rd RVPedigree/man/Estim.H0.ASKAT.Rd RVPedigree/man/Get.G.Rd RVPedigree/man/perm.hap.Rd RVPedigree/man/read.haplo.shapeit_haps.Rd RVPedigree/man/RVPedigree.Rd RVPedigree/man/VCC3.region.Rd RVPedigree/man/pvalue.NormalizedASKAT.Rd RVPedigree/man/VCC2.region.Rd RVPedigree/man/read.haplo.Rd RVPedigree/man/NormalizedASKAT.region.Rd RVPedigree/man/Estim.H0.NormalizedASKAT.Rd RVPedigree/man/VCC1.region.Rd RVPedigree/man/readMapFile.Rd RVPedigree/man/pvalue.VCC1.Rd RVPedigree/man/pvalue.VCC3.Rd RVPedigree/man/compute.weights.Rd RVPedigree/man/RVPedigree-package.Rd RVPedigree/man/read.pedigree.Rd RVPedigree/man/ASKAT.region.Rd RVPedigree/man/pvalue.VCC2.Rd RVPedigree/man/read.haplo.bedfile.Rd RVPedigree/man/Estim.H0.VCC.Rd RVPedigree/man/Preparation.hap.perm.Rd

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