Transmission/disequilibrium test of a multiallelic marker
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.
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.
References
Miller MB (1997). “Genomic scanning and the transmission/disequilibrium test: analysis of error rates.” Genet Epidemiol, 14(6), 851-6. 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. 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.
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.
Examples
if (FALSE) { # \dontrun{
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)
} # }