coreTDT (version 1.0)

coreTDT: Transimission Disequilibrium Test for compound heterozygous and recessive models

Description

This program is used to compute the pvalues for Transimission Disequilibrium Test for compound heterozygous and recessive models

Usage

coreTDT_geneset(samplePed, controlInf, useControlMAF = TRUE, maf.threshold = 1,
				 qc.proportion = 0.8, geneList = c(), 
				 outputFile = "coreTDT_analysis.out",
				 chrX = FALSE,writeFile=FALSE)
coreTDT_single(ped, maf.threshold = 1, qc.proportion = 0.8, 
				geneid = NA,control.maf = NULL)

Arguments

samplePed

plink file to input genetype informations, ref to PLINK recodeA

controlInf

Files form ATAV,contain information about variants,(evs dataset used)

useControlMAF

logical, if true, remove the variants with control MAF >= maf.threshold, else use parents MAF

maf.threshold

The allowed maximum of MAF that variants will be used in computation

qc.proportion

variants that have more than qc.proportion families with enough coverage will be used in computation

geneList

a vector containing gene names that used to analysis

outputFile

output file name

chrX

logical, if true, analyse chromosome X, not activated yet

writeFile

logical, if true, write the results to outputFile

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

geneid

character, gene name

control.maf

vector contain the MAF of each variant in controls

Value

pvalue_pr

pvalues computed from probabaility model

pvalue_lr

pvalues from likelihood ratio test with restricted alternative hypothesis

pvalue_lr2

pvalues from likelihood ratio test

nmissing

number of variants is missing in data

nMedErr

number of loci contain mendel errors

nfamily

sample size

nsnp

number of variants used in analysis

N11

number of family with parents compound genotype 1,1

N12

number of family with parents compound genotype 1,2

N112

number of family with compound genotype 1,1,2

N122

number of family with compound genotype 1,2,2

References

Yu Jiang, Janice M McCarthy, Andrew S Allen,Testing the effect of rare compound-heterozygous and recessive mutations in case-parent sequencing studies (In Preparation)

Examples

data(coreTDTexample)
attach(coreTDTexample)	
coreTDT_geneset(samplePed, controlInf,maf.threshold=0.05,writeFile=FALSE)