MCPDT {MCPDT}R Documentation

Monte Carlo Pedigree Disequilibrium Test (MCPDT) and Monte Carlo Pedigree Parental-Asymmetry Test (MCPPAT)

Description

Pedigree disequilibrium test (PDT) and pedigree parental-asymmetry test (PPAT) with missing genotypes simulated conditioned on observed genotypes.

Usage

  MCPDT(ped,mcsize,loci=NULL,af=NULL,sexlinked=FALSE)

  MCPPAT(ped,mcsize,loci=NULL,af=NULL,sexlinked=FALSE)

Arguments

ped name of a standard LINKAGE pedigree file (pre-makeped format) or a matrix/dataframe containing the pedigree data
mcsize Monte Carlo sample size
loci name of a standard LINKAGE loci file
af matrix of marker allele frequencies, one column for each marker
sexlinked whether the markers are on X chromosome

Details

‘MCPDT’ calculates PDT and MCPDT statistics and p-values.

‘MCPPAT’ calculates PDT, MCPDT, PPAT and MCPPAT statistics and p-values.

ped is required. Only SNP markers are supported. If loci file is provided, allele frequencies are read from the file specified. Otherwise, they can be provided directly in the argument af. If allele frequencies are not provided in either way, they are estimated from all the typed founders' genotypes.

If there are multiple markers, each marker is analyzed separately.

sexlinked only applies to MCPDT since MCPPAT only deals with autosomal markers. If sexlinked=TRUE in ‘MCPPAT’, only PDT and MCPDT will be calculated.

Value

Tstat PDT T statistics for the markers
pvalue P values assuming asymptotic normal distribution
mcsize Monte Carlo sample size
af allele frequencies used in the simulation

References

Martin, E. R., Monks, S. A., Warren, L. L. and Kaplan, N. L. (2000) A test for linkage and association in general pedigrees: the pedigree disequilibrium test. Am J Hum Genet 67:146-154

Ding, J., Lin, S. and Liu, Y. (2006) Monte Carlo pedigree disequilibrium test for markers on the X chromosome. Am J Hum Genet 79:567-573

Zhou, J.Y., Ding, J., Fung, W.K. and Lin, S. (2009) Detection of parent-of-origin effects using general pedigree data. Submitted

Ott, J. (1989) Computer-simulation methods in human linkage analysis. Proc Natl Acad Sci USA 86:4175-4178

Weeks, D. E., Ott, J., and Lathrop, G. M. (1990) SLINK: A general simulation program for linkage analysis. Am J Hum Genet 47:A204

Examples






[Package MCPDT version 0.2-1 Index]