rvTDT: population control weighted rare-varaints TDT

In rvTDT: population control weighted rare-variants TDT

Description

Used to compute population controls weighted rare variants transmission distortion test

Usage

	rvTDT(ped,evs,maf.threshold=1,qc.proportion=0.8)

Arguments

ped	contain the genotype information for all samples,assume m families and n snps, 3m * n matrix, each column represents a variant, coded by 0/1/2 (number of alternative alleles);each row represents a sample, the first m rows are for child,the second m rows are for mother,the last m rows are for father
evs	coontain the control information from evs,4 columns: rowname: varaint's ID: chr_pos_ref_alt; col1: number of samples have genotype 2;col2: number of samples have genotype 1;col3: number of samples have genotype 0;col4: mean coverage at this locus
maf.threshold	The allowed maximum of MAF that variants will be used in computation, for unweighted and weighted by MAF, the MAF is computed through parents genotype while weighted by population controls, the maf is computed through population controls
qc.proportion	variants that have more than qc.proportion families with enough coverage will be used in computation

Details

Package:	rvTDT
Type:	Package
Version:	1.0
Date:	2014-04-07
License:	GPL-3

Value

An object of class rvTDT,basically a list including elements:

nfamily	number of total families in computation
nsnptot	the total number of snps that in the input files
nsnpcompute	the number of snps that pass the QC
p_lc_1	p value of unweighted linear combinated TDT
p_lc_maf	p value of linear combinated TDT weighted by MAF (dbeta(1,25,maf))
p_lc_pc	p value of linear combinated TDT weighted by population controls
p_k_1	p value of unweighted kernel TDT
p_k_maf	p value of kernel TDT weighted by MAF (dbeta(1,25,maf))
p_k_pc	p value of kernel TDT weighted by population controls

Author(s)

Yu Jiang, Andrew S. Allen

Maintainer: Yu Jiang <[e-mail]>

References

Yu Jiang, Glen A. Satten, Yujun Han, Michael P. Epstein, Erin L. Heinzen, David B. Goldstein, Andrew S. Allen; Utilizing Population Controls in Rare-Variant Case-Parent Association Tests

Examples

data(rvTDT.example)
attach(rvTDT.example)	
rvTDT(ped,evs,maf.threshold=1)

rvTDT documentation built on May 2, 2019, 9:26 a.m.