SNPs

<p>SNPs data.frame contains selected SNPs and other clinical covariates for cases and controls 
    in a case-control study</p>
<p>SNPs.info.pos data.frame contains the names of the SNPs included in the data set 'SNPs' including
    their chromosome and their genomic position</p>

datasets

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

SNPs function

<p>'SNPs' data.frame contains the following columns:</p><table class="table">
<tr><td>id</td><td>identifier of each subject</td></tr>
<tr><td>casco</td><td>case or control status: 0-control, 1-case</td></tr>
<tr><td>sex</td><td>gender: Male and Female</td></tr>
<tr><td>blood.pre</td><td>arterial blood presure</td></tr>
<tr><td>protein</td><td>protein levels</td></tr>
<tr><td>snp10001</td><td>SNP 1</td></tr>
<tr><td>snp10002</td><td>SNP 2</td></tr>
<tr><td>...</td><td>...</td></tr>
<tr><td>snp100036</td><td>SNP 36</td></tr>
</table><p></p><p></p>

Format

SNPs in a case-control study — SNPs

<p>'SNPs' data.frame contains the following columns:</p><table class='table'>
<tr><td>id</td><td>identifier of each subject</td></tr>
<tr><td>casco</td><td>case or control status: 0-control, 1-case</td></tr>
<tr><td>sex</td><td>gender: Male and Female</td></tr>
<tr><td>blood.pre</td><td>arterial blood presure</td></tr>
<tr><td>protein</td><td>protein levels</td></tr>
<tr><td>snp10001</td><td>SNP 1</td></tr>
<tr><td>snp10002</td><td>SNP 2</td></tr>
<tr><td>...</td><td>...</td></tr>
<tr><td>snp100036</td><td>SNP 36</td></tr>
</table>



SNPs: SNPs in a case-control study

Description

Usage

Arguments

Format

id	identifier of each subject
casco	case or control status: 0-control, 1-case
sex	gender: Male and Female
blood.pre	arterial blood presure
protein	protein levels
snp10001	SNP 1
snp10002	SNP 2
...	...
snp100036	SNP 36