colPOlrt: Parent-of-Origin Tests

In trio: Testing of SNPs and SNP Interactions in Case-Parent Trio Studies

Description

Computes the test statistics and the corresponding p-values either for the Parent-of-Origin Likelihood Ratio Test proposed by Weinberg (1999) or the Transmission Asymmetry Test proposed by Weinberg et al. (1998).

Usage

colPOlrt(mat.snp, size = 20)
   
colTAT(mat.snp, stratified = FALSE, size = 50, bothHet = 0) 

## S3 method for class 'polrt'
print(x, top = 5, digits = 4, ...)

## S3 method for class 'tat'
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 test statistics.
stratified	should also test statistics and p-values stratified by paternal and maternal transmission be computed?
bothHet	a numeric value between 0 and 1 specifying how trios in which both parents are heterozygous are weighted in determination of the TAT statistic. By default, such trios are ignored (as proposed by Weinberg, 1999). If bothHet = 1, such trios are treated in the same way as trios with one heterozygous parent. Other values (e.g., bothHet = 0.5) are also sometimes used for bothHet.
x	an object of class polrt or tat, i.e. the output of colPOlrt or colTAT, respectively.
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

For colPOlrt, an object of class polrt consisting of the following numeric vectors:

stat	the values of the test statistic of the likelihood ratio test for all SNPs in mat.snp,
pval	the corresponding p-values,
full	the values of the maximized likelihoods of the full models containing also a parameter for the parent-of-origin effect,
red	the values of the maximied likelihoods of the reduced models not containing this parameter.

For colTAT, an object of class tat consisting of the following numeric vectors:

stat	the values of the test statistic of transmission asymmetry test for all SNPs in mat.snp,
pval	the corresponding p-values,
usedTrios	the number of trios affecting the determination of the TAT statistic,

and if stratified = TRUE

matStrat	a matrix with four columns containing the number of minor alleles transmitted and not-transmitted by heterozygous fathers and mothers,
statPaternal	a numeric vector containing for each SNP the value of the test statistic for testing whether the numbers of paternal transmissions and non-transmissions differ,
pvalPaternal	the p-values corresponding to statPaternal,
statMaternal	a numeric vector containing for each SNP the value of the test statistic for testing whether the numbers of maternal transmissions and non-transmissions differ,
pvalMaternal	the p-values corresponding to statMaternal.

Author(s)

Holger Schwender, [e-mail]

References

Weinberg, C.R.,Wilcox, A.J., and Lie, R.T. (1998). A Log-Linear Approach to Case-Parent-??Triad Data: Assessing Effects of Disease Genes that act Either Directly or Through Maternal Effects and that may be Subject to Parental Imprinting. American Journal of Human Genetics, 62, 969-978.

Weinberg, C.R. (1999). Methods for Detection of Parent-of-Origin Effects in Genetic Studies of Case-Parents Triads. American Journal of Human Genetics, 65, 229-235.

See Also

colTDT, ped2geno

Examples

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

# The Parent-of-Origin Likelihood Ratio Test can be applied
# to the SNPs in mat.test by
po.out <- colPOlrt(mat.test)

# The Transmission Asymmetry Test can be applid to the SNPs
# in mat.test by 
tat.out <- colTAT(mat.test)

# By default, statistics for the top 5 SNPs are displayed.
# If another number of SNPs, say 10, should be displayed,
# then this can be done by
print(po.out, top = 10)

# The statistics for all SNPs (not ordered by their 
# significance) can be obtained by
print(po.out, top = 0)

Example output

         Parent-Of-Origin Likelihood Ratio Test

     LL (with) LL (without) Statistic P-Value
SNP1    -43.58       -44.19    1.2163  0.2701
SNP2    -38.55       -38.64    0.1882  0.6645
SNP3    -37.39       -37.93    1.0728  0.3003
SNP4    -37.92       -38.15    0.4693  0.4933
SNP5    -40.22       -40.49    0.5477  0.4593
SNP6    -40.57       -40.63    0.1222  0.7267
         Parent-Of-Origin Likelihood Ratio Test

     LL (with) LL (without) Statistic P-Value
SNP1    -43.58       -44.19    1.2163  0.2701
SNP2    -38.55       -38.64    0.1882  0.6645
SNP3    -37.39       -37.93    1.0728  0.3003
SNP4    -37.92       -38.15    0.4693  0.4933
SNP5    -40.22       -40.49    0.5477  0.4593
SNP6    -40.57       -40.63    0.1222  0.7267

trio documentation built on Nov. 8, 2020, 7:41 p.m.