RVPedigree: Methods for Family-Based Rare-Variant Genetic Association Tests
Version 0.0.3

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("RVPedigree")

Getting started

Package overview

Popular man pages

Estim.H0.ASKAT: Estimation of the variance components under the null model...
Estim.H0.NormalizedASKAT: Estimation of the variance components under the null model...
Get.G: Create genotypes from haplotypes
GetRelMatrix: Estimate relationship matrix based on pedigree or genomic...
NormalizedASKAT.region: Run the normalized ASKAT method on a genomic region defined...
perm.hap: Permute haplotypes
RVPedigree: RVPedigree main function
See all...

All man pages Function index File listing

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...

Functions

ASKAT.region Man page Source code
Estim.H0.ASKAT Man page Source code
Estim.H0.NormalizedASKAT Man page Source code
Estim.H0.VCC Man page Source code
Get.G Man page Source code
GetRelMatrix Man page Source code
Neg.LogLikelihood.ASKAT Source code
Neg.LogLikelihood.VC.C1 Source code
Normality.test Man page Source code
NormalizedASKAT.region Man page Source code
Preparation.VCC Man page Source code
Preparation.hap.perm Man page Source code
RVPedigree Man page Source code
RVPedigree-package Man page
VCC1.region Man page Source code
VCC2.region Man page Source code
VCC3.region Man page Source code
check_Ncores Source code
check_VCC3afterVCC1 Source code
check_covariates Source code
check_files Source code
check_method Source code
check_pheno Source code
check_positions Source code
check_regions Source code
check_relmatrix Source code
check_weights Source code
compute.weights Man page Source code
ff Source code
findParentIndices Source code
meiose Source code
perm.hap Man page Source code
pvalue.ASKAT Man page Source code
pvalue.NormalizedASKAT Man page Source code
pvalue.VCC1 Man page Source code
pvalue.VCC2 Man page Source code
pvalue.VCC3 Man page Source code
read.haplo Man page Source code
read.haplo.bedfile Man page Source code
read.haplo.pedfile Man page Source code
read.haplo.shapeit_haps Man page Source code
read.pedigree Man page Source code
readMapFile Man page Source code

Files

inst
inst/CITATION
inst/extdata
inst/extdata/genes.lst
inst/extdata/test.map
inst/extdata/data_nullmorgans.map
inst/extdata/dataT.tfam
inst/extdata/data.map
inst/extdata/test.bed
inst/extdata/genes2.lst
inst/extdata/covariates.dat
inst/extdata/gwaa.data.RData
inst/extdata/dataB.bed
inst/extdata/pheno.dat
inst/extdata/data.phe
inst/extdata/NNormTrait.dat
inst/extdata/data.ped
inst/extdata/test.ped
inst/extdata/test.bim
inst/extdata/OneFamilyExample.ped
inst/extdata/covariates2.dat
inst/extdata/kinmat.Rdata
inst/extdata/TwoFamilyExample.ped
inst/extdata/test.fam
inst/extdata/dataB.bim
inst/extdata/dataT.tped
inst/extdata/dataB.fam
inst/doc
inst/doc/vignette.Rnw
inst/doc/vignette.pdf
inst/doc/vignette.R
NAMESPACE
R
R/read.haplo.R
R/VCC3.region.R
R/RVPedigree-package.R
R/pvalue.NormalizedASKAT.R
R/pvalue.VCC3.R
R/read.haplo.bedfile.R
R/pvalue.VCC1.R
R/VCC2.region.R
R/Neg.LogLikelihood.ASKAT.R
R/Estim.H0.VCC.R
R/read.pedigree.R
R/Normality.test.R
R/VCC1.region.R
R/Estim.H0.NormalizedASKAT.R
R/Get.G.R
R/Preparation.hap.perm.R
R/Neg.LogLikelihood.VC.C1.R
R/NormalizedASKAT.region.R
R/Preparation.VCC.R
R/ASKAT.region.R
R/read.haplo.shapeit-haps.R
R/inputChecks.R
R/pvalue.ASKAT.R
R/compute.weights.R
R/pvalue.VCC2.R
R/GetRelMatrix.R
R/Estim.H0.ASKAT.R
R/meiose.R
R/perm.hap.R
R/RVPedigree.R
R/findParentIndices.R
R/readMapFile.R
R/read.haplo.pedfile.R
vignettes
vignettes/vignette.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/GetRelMatrix.Rd
man/pvalue.ASKAT.Rd
man/Normality.test.Rd
man/Preparation.VCC.Rd
man/read.haplo.pedfile.Rd
man/Estim.H0.ASKAT.Rd
man/Get.G.Rd
man/perm.hap.Rd
man/read.haplo.shapeit_haps.Rd
man/RVPedigree.Rd
man/VCC3.region.Rd
man/pvalue.NormalizedASKAT.Rd
man/VCC2.region.Rd
man/read.haplo.Rd
man/NormalizedASKAT.region.Rd
man/Estim.H0.NormalizedASKAT.Rd
man/VCC1.region.Rd
man/readMapFile.Rd
man/pvalue.VCC1.Rd
man/pvalue.VCC3.Rd
man/compute.weights.Rd
man/RVPedigree-package.Rd
man/read.pedigree.Rd
man/ASKAT.region.Rd
man/pvalue.VCC2.Rd
man/read.haplo.bedfile.Rd
man/Estim.H0.VCC.Rd
man/Preparation.hap.perm.Rd
RVPedigree documentation built on May 19, 2017, 8:55 p.m.

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