allelicTDT {trio} | R Documentation |
Performs the allelic Transmission/Disequilibrium Test for each SNP contained in a genotype matrix.
allelicTDT(mat.snp, size = 50, correct = FALSE) ## S3 method for class 'aTDT' print(x, top = 5, digits = 4, ...)
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 |
size |
the number of SNPs considered simultaneously when computing the parameter estimates. |
correct |
should the test statistic be continuity corrected? If |
x |
an object of class |
digits |
number of digits that should be printed. |
top |
number of interactions that should be printed. If |
... |
ignored. |
An object of class aTDT
containing the following numeric vectors:
stat |
values of the test statistic of the allelic TDT, |
pval |
the corresponding p-values. |
Holger Schwender, holger.schwender@udo.edu
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.
# 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)