snp.all2

A dataset containing the list of variables in the PLINK files
The variables are as follows:

datasets

Simulate genotypes for case-parent triads, case-control, and quantitative trait samples with realistic linkage diequilibrium structure and allele frequency distribution. For studies of epistasis one can simulate models that involve specific SNPs at specific sets of loci, which we will refer to as "pathways". TriadSim generates genotype data by resampling triad genotypes from existing data. The details of the method is described in the manuscript under preparation "Simulating Autosomal Genotypes with Realistic Linkage Disequilibrium and a Spiked in Genetic Effect" Shi, M., Umbach, D.M., Wise A.S., Weinberg, C.R.

Min Shi

TriadSim

Simulating Triad Genomewide Genotypes

snp.all2 function

A data frame with 10279 rows and 12 variables:<dl class="dl-horizontal">
 <dt>ord</dt><dd>Ordering of the SNPs</dd>
 <dt>RS</dt><dd>SNP rs number</dd>
 <dt>CHR</dt><dd>Chromosome</dd>
 <dt>POS</dt><dd>Chromosomal position</dd>
 <dt>A1</dt><dd>A1 allele</dd>
 <dt>A2</dt><dd>A2 allele</dd>
 <dt>MAF</dt><dd>Minor allele frequency</dd>
 <dt>NCHROBS</dt><dd>Number of observed chromosomes used in MAF calculation</dd>
</dl>

Format

SNPs in the PLINK files — snp.all2

A data frame with 10279 rows and 12 variables:<dl class='dl-horizontal'>
 <dt>ord</dt><dd>Ordering of the SNPs</dd>
 <dt>RS</dt><dd>SNP rs number</dd>
 <dt>CHR</dt><dd>Chromosome</dd>
 <dt>POS</dt><dd>Chromosomal position</dd>
 <dt>A1</dt><dd>A1 allele</dd>
 <dt>A2</dt><dd>A2 allele</dd>
 <dt>MAF</dt><dd>Minor allele frequency</dd>
 <dt>NCHROBS</dt><dd>Number of observed chromosomes used in MAF calculation</dd>
</dl>

snp.all2: SNPs in the PLINK files

Description

Usage

Arguments

Format