rvPDT.test.permu {rvHPDT}

Variants-based pedigree disequilibrium test for rare variants in pedigrees.

Description

To detecting rare variants for binary traits using general pedigrees, the pedigree disequilibrium tests are extended by collapsing rare variants with/without weights.

Usage

rvPDT.test.permu(ped, aff=2,unaff=1, snpCol, hfreq=NULL,
useFamWeight=TRUE, nperm=1000,trace=FALSE)    

Arguments

ped

input data, has same format with PLINK but having column names. The PED file is a white-space (space or tab) delimited file: the first six columns are mandatory: FID: Family ID; IID: Individual ID; FA: Paternal ID; MO: Maternal ID; SEX: Sex (1=male; 2=female; other=unknown); PHENO: Phenotype; Genotypes (column 7 onwards) should also be white-space delimited; they are coded as 0, 1 and 2, indicating the number of coding allele, and NA is for missing genotype.

aff

indicates the values that represents affected status in ped data; default is 2.

unaff

indicates the values that represents unaffected status in ped data; default is 1.

snpCol

indicates the columns of variants in ped data.

hfreq

indicates the frequencies of variants that used in calculating weights; when it is NULL, the frequencies are estimated by ped data.

useFamWeight

indicates whether the family weights need to be used in the test.

nperm

indicates the times of permutation; default is 1000.

trace

indicates wether or not the intermediate outcomes should be printed; default is FALSE.

Value

TDT

Transmission/disequilibrium matrix for each pedigrees.

Sib

Discordant sib pairs matrix for each pedigrees.

PDT

Pedigree disequilibrium matrix for each pedigrees, which is the sum of TDT and Sib.

W

Weights used in Weighted rvPDT test.

test.v1

Weighted rvPDT test statistic with weights W.

test.v0

Unweighted rvPDT test statistic with weights=1.

pvalue.v1

P value of weighted rvPDT test statistic (test.v1).

pvalue.v0

P value of unweighted rvPDT test statistic (test.v0).

References

Guo W , Shugart YY, Does Haplotype-based Collapsing Tests Gain More Power than Variant-based Collapsing Tests for Detecting Rare Variants in Pedigrees (manuscript).