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.

Install the latest version of this package by entering the following in R:
install.packages("RVPedigree")
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...

Functions

ASKAT.region Man page
compute.weights Man page
Estim.H0.ASKAT Man page
Estim.H0.NormalizedASKAT Man page
Estim.H0.VCC Man page
Get.G Man page
GetRelMatrix Man page
Normality.test Man page
NormalizedASKAT.region Man page
perm.hap Man page
Preparation.hap.perm Man page
Preparation.VCC Man page
pvalue.ASKAT Man page
pvalue.NormalizedASKAT Man page
pvalue.VCC1 Man page
pvalue.VCC2 Man page
pvalue.VCC3 Man page
read.haplo Man page
read.haplo.bedfile Man page
read.haplo.pedfile Man page
read.haplo.shapeit_haps Man page
readMapFile Man page
read.pedigree Man page
RVPedigree Man page
RVPedigree-package Man page
VCC1.region Man page
VCC2.region Man page
VCC3.region Man page

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.