allelicTDT: Allelic TDT

Description

Performs the allelic Transmission/Disequilibrium Test for each SNP contained in a genotype matrix.

Usage

allelicTDT(mat.snp, size = 50, correct = FALSE)
"print"(x, top = 5, digits = 4, ...)

Arguments

mat.snp

a numeric matrix in which each column represents a SNP. Each column must be a numeric vector of length $3 * t$ representing a SNP genotyped at $t$ trios. Each of the $t$ blocks must consist of the genotypes of father, mother, and offspring (in this order). The genotypes must be coded by 0, 1, and 2. Missing values are allowed and need to be coded by NA. This matrix might be generated from a ped-file by, e.g., employing ped2geno.

size

the number of SNPs considered simultaneously when computing the parameter estimates.

correct

should the test statistic be continuity corrected? If FALSE, $(b-c)^2 / (b+d)$ will be used as test statistic, where $b$ and $c$ are the off-diagonal elements of the 2x2-table summarizing the transmitted and not transmitted alleles from the heterozygous parents. If TRUE, $(|b-c| - 1)^2 / (b+d)$ will be used as test statistic.

an object of class aTDT, i.e. the output of allelicTDT.

digits

number of digits that should be printed.

top

number of interactions that should be printed. If top is less than or equal to zero, set to NA, or larger than the number of SNPs, then the statistics for all SNPs are printed in the order as they were in the genotype matrix used as input into colTDT. Otherwise, the top interactions with the smallest p-values are printed.

...

ignored.

Value

stat: values of the test statistic of the allelic TDT,
pval: the corresponding p-values.

References

Spielman, R.S., McGinnis, R.E., and Ewens, W.J. (1993). Trsnmmission Test for Linkage Disequilibrium: The Insulin Gene Region and Insulin-Dependent Diabetes Mellitus (IDDM). American Journal of Human Genetics, 52, 506-516.

Examples

Run this code

# Load the simulated data for the analysis.
data(trio.data)

# Perform an allelic TDT
a.out <- allelicTDT(mat.test)

# By default, the top 5 SNPs are shown.
# Another number of SNPs, e.g., 10, are displayed by
print(a.out, top=10)

# If the results for all SNPs should be shown (or returned), use
print(a.out, top=0)