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gap

mtdt

Transmission/disequilibrium test of a multiallelic marker

Description

This function calculates transmission-disequilibrium statistics involving multiallelic marker.

Inside the function are tril and triu used to obtain lower and upper triangular matrices.

Usage

mtdt(x,n.sim=0)

Arguments

`x`	the data table
`n.sim`	the number of simulations

Value

It returned list contains the following components:

`SE`	Spielman-Ewens Chi-square from the observed data
`ST`	Stuart or score Statistic from the observed data
`pSE`	the simulated p value
`sSE`	standard error of the simulated p value
`pST`	the simulated p value
`sST`	standard error of the simulated p value

References

Miller MB (1997) Genomic scanning and the transmission/disequilibrium test: analysis of error rates. Genet. Epidemiol. 14:851-856

Sham PC (1997) Transmission/disequilibrium tests for multiallelic loci. Am. J. Hum. Genet. 61:774-778

Spielman RS, Ewens WJ (1996) The TDT and other family-based tests for linkage disequilibrium and association. Am. J. Hum. Genet. 59:983-989

Zhao JH, Sham PC, Curtis D (1999) A program for the Monte Carlo evaluation of significance of the extended transmission/disequilibrium test. Am. J. Hum. Genet. 64:1484-1485

Author(s)

Mike Miller, Jing Hua Zhao

Examples

## Not run: 
# Copeman et al (1995) Nat Genet 9: 80-5

x <- matrix(c(0,0, 0, 2, 0,0, 0, 0, 0, 0, 0, 0,
              0,0, 1, 3, 0,0, 0, 2, 3, 0, 0, 0,
              2,3,26,35, 7,0, 2,10,11, 3, 4, 1,
              2,3,22,26, 6,2, 4, 4,10, 2, 2, 0,
              0,1, 7,10, 2,0, 0, 2, 2, 1, 1, 0,
              0,0, 1, 4, 0,1, 0, 1, 0, 0, 0, 0,
              0,2, 5, 4, 1,1, 0, 0, 0, 2, 0, 0,
              0,0, 2, 6, 1,0, 2, 0, 2, 0, 0, 0,
              0,3, 6,19, 6,0, 0, 2, 5, 3, 0, 0,
              0,0, 3, 1, 1,0, 0, 0, 1, 0, 0, 0,
              0,0, 0, 2, 0,0, 0, 0, 0, 0, 0, 0,
              0,0, 1, 0, 0,0, 0, 0, 0, 0, 0, 0),nrow=12)

# See note to bt for the score test obtained by SAS

mtdt(x)

## End(Not run)

gap

Genetic Analysis Package

v1.2.3-1

GPL (>= 2)

Authors

Jing Hua Zhao and colleagues with inputs from Kurt Hornik and Brian Ripley

Initial release

2021-4-21