inheritance

geneticModel

codominant

dominant

recessive

overdominant

additive

categorical covariate having genotypes

codominant function recodifies a variable having genotypes depending on the allelic frequency
 in descending order. 
dominant, recessive, and overdominant functions collapse the three categories of a given SNP 
 into two categories as follows: Let 'AA', 'Aa', and 'aa' be the three genotypes. After determining
 the most frequent allele (let's suppose that 'A' is the major allele) the functions return a vector
 with to categories as follows. dominant: 'AA' and 'Aa-aa'; recessive: 'AA-Aa' and 'aa'; 
 overdominant: 'AA-aa' vs 'Aa'. 
additive function creates a numerical variable, 1, 2, 3 corresponding to the three genotypes sorted
 out by descending allelic frequency (this model is referred as log-additive).

utilities

Functions to perform most of the common analysis in genome association studies are implemented. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated. The methods are described in Gonzalez JR et al., 2007 <doi: 10.1093/bioinformatics/btm025>.

Juan Gonzalez

SNPassoc

SNPs-Based Whole Genome Association Studies

Victor Moreno

Juan R Gonzalez

inheritance function

<dl> <dt>o</dt>
<dd>categorical covariate having genotypes</dd></dl>

Arguments

codominant function recodifies a variable having genotypes depending on the allelic frequency
 in descending order. 
dominant, recessive, and overdominant functions collapse the three categories of a given SNP 
 into two categories as follows: Let 'AA', 'Aa', and 'aa' be the three genotypes. After determining
 the most frequent allele (let's suppose that 'A' is the major allele) the functions return a vector
 with to categories as follows. dominant: 'AA' and 'Aa-aa'; recessive: 'AA-Aa' and 'aa'; 
 overdominant: 'AA-aa' vs 'Aa'. 
additive function creates a numerical variable, 1, 2, 3 corresponding to the three genotypes sorted
 out by descending allelic frequency (this model is referred as log-additive).

Collapsing (or recoding) genotypes into different categories (generally two) depending on a given genetic mode of inheritance — inheritance

<dl>

 <dt>o</dt>
<dd>categorical covariate having genotypes</dd>

</dl>

inheritance: Collapsing (or recoding) genotypes into different categories (generally two) depending on a given genetic mode of inheritance

Description

Usage

Value

Arguments

Examples