genotypes: Simulated genotypes

In epiGWAS: Robust Methods for Epistasis Detection

Description

We simulated 300 unphased European genotypes. For that matter, we used the HAPGEN2 software and the 1000 genome phase 3 reference data. The simulated regions are located on the 22 chromosome between the nucleotide positions 16061016 (rs9617528) and 19976834 (rs887201). Only the markers of the Affymetrix 500K are included.

Usage

data(genotypes)

Format

An integer matrix with 300 rows and 450 columns. The SNP rsIDs and positions, in addition to their reference and alternate alleles, are combined in colnames(X).

References

Su, Z., Marchini, J., & Donnelly, P. (2011). HAPGEN2: Simulation of multiple disease SNPs. Bioinformatics, 27(16), 2304–2305.

Consortium, T. 1000 G. P., Auton, A., Abecasis, G. R., Altshuler (Co-Chair), D. M., Durbin (Co-Chair), R. M., Abecasis, G. R., … Abecasis, G. R. (2015). A global reference for human genetic variation. Nature, 526, 68.

Examples

data(genotypes)

hmm <- fast_HMM(genotypes, fp_path = '/path/to/fastPHASE')

epiGWAS documentation built on Sept. 8, 2019, 5:02 p.m.