mtdt2: Transmission/disequilibrium test of a multiallelic marker by Bradley-Terry model

Description

This function calculates transmission-disequilibrium statistics involving multiallelic marker according to Bradley-Terry model.

Usage

mtdt2(x, verbose=TRUE, n.sim=NULL, ...)

Arguments

the data table

verbose

To print out test statistics if TRUE

n.sim

Number of simulations

...

other options compatible with the BTm function

Value

It returned list contains the following components:
c2bA data frame in four-column format showing transmitted vs nontransmitted counts
BTmA fitted Bradley-Terry model object
X2Allele-wise, genotype-wise and goodness-of-fit Chi-squared statistics
dfDegrees of freedom
pP value
pnMonte Carlo p values when n.sim is specified

References

Firth, D. (2005). Bradley-terry models in R. Journal of Statistical Software 12(1):1-12

Sham PC, Curtis D (1995) An extended transmission/disequilibrium test (TDT) for multi-allelic marker loci. Ann. Hum. Genet. 59:323-336

Turner H, Firth D (2010) Bradley-Terry models in R: The BradleyTerry2 package. http://cran.r-project.org/web/packages/BradleyTerry2/vignettes/BradleyTerry.pdf.

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

Run this code

# 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)

xx <- mtdt2(x,refcat="12")