| lrtG {IFP} | R Documentation |
Likelihood Ratio Tests for Identifying Disease Polymorphisms with Same Effects
Description
Compute p-values and likelihoods of all possible models for a given number of disease SNP(s).
Usage
lrtG(n.fp, genoT, genoC)
Arguments
n.fp |
number of disease SNPs for tests. |
genoT |
matrix of control genotypes. Each row indicates a variant, and each column indicates a haplotype of an individual. Two alleles of 0 and 1 are allowed. |
genoC |
matrix of case genotypes. Each row indicates a variant, and each column indicates a haplotype of an individual. Two alleles of 0 and 1 are allowed. |
Value
matrix of likelihood ratio test results. First row indicates the index, and following n.fp rows indicate the model for each set of disease polymorphisms, and followed by p-values, -2 log(likelihood ratio) with corrections for variances, and the degree of freedom.
References
L. Park, J. Kim, Rare high-impact disease variants: properties and identification, Genetics Research, 2016 Mar; 98, e6.
See Also
allele.freq.G
Examples
## LRT tests for a dominant variant (15th variant)
## the odds ratio: 3, control: 100, case: 100.
data(apoeG)
lrtG(1,genoT[,1:20],genoC[,1:20])
# use "lrtG(1,genoT,genoC)" for the actual test.