Transmission/disequilibrium test of a multiallelic marker by 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.

Details

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

References

Firth D (2005). “Bradley-Terry Models in R.” Journal of Statistical Software, 12(1), 1 - 12. doi:10.18637/jss.v012.i01 .

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

Author

Jing Hua Zhao keywords models keywords htest

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)

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