gap: mtdt2 – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

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

`x`	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:

`c2b`	A data frame in four-column format showing transmitted vs nontransmitted counts
`BTm`	A fitted Bradley-Terry model object
`X2`	Allele-wise, genotype-wise and goodness-of-fit Chi-squared statistics
`df`	Degrees of freedom
`p`	P value
`pn`	Monte 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

Author(s)

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)

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

## 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