colTDTmaxTest: Maximum Genotypic TDT

Description

Computes the maximum over the gTDT statistics for an additive, dominant, and recessive model. colTDTmaxTest additionally computes permutation-based p-values.

Usage

colTDTmaxTest(geno, perm = 10000, size = 50, chunk = 10000,  minimum = 0.001, verbose = FALSE)
colTDTmaxStat(geno, size = 50)
"print"(x, top = 5, digits = 4, ...)
"print"(x, top = 5, digits = 4, ...)

Arguments

geno

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.

perm

number of permutations of the response for which the permuted values of the test statistic should be computed.

size

number of SNPs that should be considered simultaneously when estimating the parameter.

chunk

number of permutations that should be considered simultaneously in the computation of the p-values

minimum

minimum value that a test statistic must show that for the corresponding SNP the p-value is computed.

verbose

logical indicating whether some information on what is currently computed should be printed.

an object of class maxTestTrio or maxTestStat, i.e. the output of colTDTmaxTest or of colTDTmaxStat.

digits

number of digits that should be printed.

top

number of interactions that should be printed. If the number of interactions is smaller than or equal to top, then the statistics for all interactions are printed in the order of their computation. Otherwise, they the top Top interactions are printed.

...

ignored.

Value

For colTDTmaxStat, an object of class maxStatTrio consisting of a vector stat containing the values of the Max statistic for the SNPs in geno, a matrix max.stat containing the values of the gTDT statistic for testing an additive, a dominant, and a recessive effect, and additional information required by colTDTmaxTest.For colTDTmaxTest, an object of class maxTestTrio consisting of stat, max.stat, and the unadjusted p-values pval corresponding to stat.

References

Schwender, H., Taub, M.A., Beaty, T.H., Marazita, M.L., and Ruczinski, I. (2011). Rapid Testing of SNPs and Gene-Environment Interactions in Case-Parent Trio Data Based on Exact Analytic Parameter Estimation. Biometrics, 68, 766-773.

Examples

Run this code

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

# Perform a MAX test by only computing the MAX statistics.
max.out <- colTDTmaxStat(mat.test)

# Permutation-based p-values are additionally computed when using
max.out2 <- colTDTmaxTest(mat.test)