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RVPedigree (version 0.0.3)

Methods for Family-Based Rare-Variant Genetic Association Tests

Description

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.

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Version

Install

install.packages('RVPedigree')

Monthly Downloads

1

Version

0.0.3

License

GPL (>= 3)

Maintainer

Karim Oualkacha

Last Published

January 20th, 2016

Functions in RVPedigree (0.0.3)

GetRelMatrix

Estimate relationship matrix based on pedigree or genomic data
compute.weights

Compute/create matrix with genotype weights
read.pedigree

Read pedigree structure from a Plink file
ASKAT.region

Run the ASKAT method on a genomic region defined by a start and a stop base pair coordinate
Preparation.hap.perm

Prepare for the haplotype permutation
readMapFile

Read file with information about SNPs chromosome and position, for example from regular PLINK .map OR .bim file
VCC1.region

Run the VC-C1 method on a genomic region defined by a start and a stop base pair coordinate
perm.hap

Permute haplotypes
NormalizedASKAT.region

Run the normalized ASKAT method on a genomic region defined by a start and a stop base pair coordinate
Estim.H0.VCC

Estimate the model parameters under the null model
pvalue.VCC3

Compute p-values for the VC-C3 method
VCC2.region

Run the VC-C2 method on a genomic region defined by a start and a stop base pair coordinate
RVPedigree-package

RVPedigree: A package for region-based genetic association tests.
Estim.H0.ASKAT

Estimation of the variance components under the null model using the ASKAT method
pvalue.VCC2

Compute the p-value for the VC-C2 method
read.haplo.bedfile

Read haplotype data, selected by region of interest, from BED files (regular PLINK binary files)
VCC3.region

Run the VC-C3 method on a genomic region defined by a start and a stop base pair coordinate
Preparation.VCC

Prepare for the VC-C methods
pvalue.ASKAT

Compute p-value and score for the ASKAT method
pvalue.VCC1

Compute score and p-value for the VC-C1 method
read.haplo

Read haplotype data, selected by region of interest, from PLINK formatted files or ShapeIt output files
Get.G

Create genotypes from haplotypes
Estim.H0.NormalizedASKAT

Estimation of the variance components under the null model using the normalized ASKAT method
RVPedigree

RVPedigree main function
Normality.test

Test for normality of the trait/phenotype
read.haplo.shapeit_haps

Read haplotype data, selected by region of interest, from a .haps file (regular ShapeIt output files)
read.haplo.pedfile

Read haplotype data, selected by region of interest, from PED files (regular PLINK untransposed text files)
pvalue.NormalizedASKAT

Compute p-value and score for the normalized ASKAT method