ped: Genotypic dataset in PED format

In waffect: A package to simulate constrained phenotypes under a disease model H1

Description

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:

• fam_id: family ID, here an integer from 1 to 100

• ind_id: individual ID, an integer from 1 to 100

• pat_id: paternal ID, here a dummy variable set to 0 for all individuals

• mat_id: maternal ID, dummy variable

• sex: all females (coded by 2)

• pheno: observed phenotypes; codes: case = 2, control = 1.

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.

Usage

data(ped)

Format

A table with 100 rows and 2007 columns.

Source

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

waffect documentation built on May 2, 2019, 6:11 a.m.