mtdt {gap}

Transmission/disequilibrium test of a multiallelic marker

Description

Transmission/disequilibrium test of a multiallelic marker

Usage

mtdt(x, n.sim = 0)

Arguments

x

the data table.

n.sim

the number of simulations.

Details

This function calculates transmission-disequilibrium statistics involving multiallelic marker. Inside the function are tril and triu used to obtain lower and upper triangular matrices.

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.

Author(s)

Mike Miller, Jing Hua Zhao

References

Miller MB (1997). “Genomic scanning and the transmission/disequilibrium test: analysis of error rates.” Genet Epidemiol, 14(6), 851-6. ISSN 0741-0395 (Print) 0741-0395, doi:10.1002/(sici)1098-2272(1997)14:6<854::aid-gepi48>3.3.co;2-7.

Sham PC, Curtis D (1995). “An extended transmission/disequilibrium test (TDT) for multi-allele marker loci.” Ann Hum Genet, 59(3), 323-36. ISSN 0003-4800 (Print) 0003-4800, doi:10.1111/j.1469-1809.1995.tb00751.x.

Spielman RS, Ewens WJ (1996). “The TDT and other family-based tests for linkage disequilibrium and association.” Am J Hum Genet, 59(5), 983-9. ISSN 0002-9297 (Print) 0002-9297.

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

## Not run: 
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)