mtdt2: Transmission/disequilibrium test of a multiallelic marker by...

In gap: Genetic Analysis Package

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

Description

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.

Details

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

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.

Author(s)

Jing Hua Zhao keywords models keywords htest

References

\insertRef

firth05gap

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

See Also

mtdt

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)

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

## End(Not run)

gap documentation built on Aug. 26, 2023, 5:07 p.m.