Description Usage Arguments Value Author(s) References See Also Examples
View source: R/colTDTmaxTest.R
Computes the maximum over the gTDT statistics for an additive, dominant, and recessive model.
colTDTmaxTest
additionally computes permutationbased pvalues.
1 2 3 4 5 6 7 8  colTDTmaxTest(geno, perm = 10000, size = 50, chunk = 10000,
minimum = 0.001, verbose = FALSE)
colTDTmaxStat(geno, size = 50)
## S3 method for class 'maxTestTrio'
print(x, top = 5, digits = 4, ...)
## S3 method for class 'maxStatTrio'
print(x, top = 5, digits = 4, ...)

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 
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 pvalues 
minimum 
minimum value that a test statistic must show that for the corresponding SNP the pvalue is computed. 
verbose 
logical indicating whether some information on what is currently computed should be printed. 
x 
an object of class 
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

... 
ignored. 
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
pvalues pval
corresponding to stat
.
Holger Schwender, holger.schwender@udo.edu
Schwender, H., Taub, M.A., Beaty, T.H., Marazita, M.L., and Ruczinski, I. (2011). Rapid Testing of SNPs and GeneEnvironment Interactions in CaseParent Trio Data Based on Exact Analytic Parameter Estimation. Biometrics, 68, 766773.
1 2 3 4 5 6 7 8  # Load the simulated data.
data(trio.data)
# Perform a MAX test by only computing the MAX statistics.
max.out < colTDTmaxStat(mat.test)
# Permutationbased pvalues are additionally computed when using
max.out2 < colTDTmaxTest(mat.test)

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