tdt.select: Select informative transmissions of sub-haplotypes for the...

In tdthap: TDT Tests for Extended Haplotypes

Select informative transmissions of sub-haplotypes for the TDT test

Description

This function is just a data handling intermediary between hap.transmit, which computes haplotypes, and tdt.quad and tdt.rr which do TDT tests.

Usage

tdt.select(hap.data, markers=1:((ncol(hap.data) - 4)/4), complete=TRUE)

Arguments

hap.data	The input dataframe. This will usually have been created by hap.transmit.
markers	An integer array indicating which loci make up the relevant part of the haplotype.
complete	If TRUE, only "complete" haplotypes are used (ie no zero's will be included).

Value

A list of two arrays of class "factor". The first (trans) contains transmitted haplotypes and the second (untrans) contains untransmitted haplotypes. Rownames identify the transmission in terms of pedigree id, offspring id, father's id, mother's id, and whether it is a paternal transmission ("f") or a maternal transmission ("m").

References

Clayton, D. and Jones, H. (1999) Transmission/disequilibrium tests for extended marker haplotypes. Am.J.Hum.Gen., 65:1161-1169.

See Also

hap.transmit, tdt.rr, tdt.quad

Examples

## Not run: 
# Select the sub-haplotype made up from the first two markers and print 
# tables of frequencies of transmitted and untransmitted haplotypes


	hap.use <- tdt.select(haps, markers=1:2)
	table(hap.use$trans)
	table(hap.use$untrans)

## End(Not run)

tdthap documentation built on Oct. 29, 2022, 1:14 a.m.