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

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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.

Author
Karim Oualkacha [aut, cre], M'Hamed Lajmi Lakhal-Chaieb [aut], Celia M.T. Greenwood [aut], Lennart C. Karssen [aut], Sodbo Sharapov [aut]
Date of publication
2016-01-20 09:12:22
Maintainer
Karim Oualkacha <oualkacha.karim@uqam.ca>
License
GPL (>= 3)
Version
0.0.3

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