gap (version 1.5-1)

mtdt: Transmission/disequilibrium test of a multiallelic marker

Description

This function calculates transmission-disequilibrium statistics involving multiallelic marker.

Usage

mtdt(x, n.sim = 0)

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

Arguments

x

the data table.

n.sim

the number of simulations.

Author

Mike Miller, Jing Hua Zhao

Details

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

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

See Also

bt

Examples

if (FALSE) {
# 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)
}