This dataset contains the genotypes of 2000 SNPs to be used with the tutorial for
 assessing the statistical power of GWAs with waffect (see the vignette). It has 100 rows (one
 for each individual) and 2007 columns:
 <ul>
<li> fam_id: family ID, here an integer from 1 to 100
 </li>
<li> ind_id: individual ID, an integer from 1 to 100
 </li>
<li> pat_id: paternal ID, here a dummy variable set to 0 for all individuals
 </li>
<li> mat_id: maternal ID, dummy variable
 </li>
<li> sex: all females (coded by 2)
 </li>
<li> pheno: observed phenotypes; codes: case = 2, control = 1. 
 </li>
</ul> Genotypes (column 7 onwards) are biallelic, one allele for each column. For instance, 
 columns 7 and 8 contain the two alleles for SNP1 and columns 9 and 10 contain the alleles
 for SNP2. Before using this dataset with PLINK it is necessary to save it into a file with 
 extension .ped (see the vignette). The genotypes were obtained from public data released by 
 the 1000 Genomes Projects.

datasets

waffect (pronounced 'double-u affect' for 'weighted
affectation') is a package to simulate phenotypic (case or
control) datasets under a disease model H1 such that the total
number of cases is constant across all the simulations (the
constrain in the title). The package also makes it possible to
generate phenotypes in the case of more than two classes, so
that the number of phenotypes belonging to each class is
constant across all the simulations. waffect is used to assess
empirically the statistical power of Genome Wide Association
studies.

G Nuel

waffect

A package to simulate constrained phenotypes under a disease
model H1

ped function

Format

1000 Genomes, A Deep Catalogue of Human Genetic Variation; http://www.1000genomes.org

ped: Genotypic dataset in PED format

Description

Usage

Arguments

Format

Source