mthfrex: Simulated example finemapping genotype and phenotype data.
In tobyjohnson/gtx: Genetics ToolboX

Description Usage Format Details Source

A simulated example finemapping genotype and phenotype dataset, consisting of genotypes for 2000 individuals at 64 SNPs, and case/control and continuous phenotypes and covariates.

1	data(mthfrex)

mthfrex is a list suitable for use with other functions in this package, see snpdata.

mthfr.params is a data frame suitable for use with other functions in this package, see gtx.params.

This is a simulated dataset, whose sole purpose is to illustrate the use of functions in this package for multi-SNP regression analyses.

The dataset is provided so that the usage examples can actually be run, without burdening each example with many lines of code to generate an analysable dataset.

The genotypes were simulated using Hudson's mksamples (ms) program, assuming an infinite sites standard neutral model with no recombination, with 1% genotypes missing at random. The simulated sites were crudely matched to real SNP names and hg18 map positions near the MTHFR locus (in an order to match rankwise with real allele frequencies). Some quasi-realistic case/control and continuous phenotypes and covariates were simulated conditional on the genotype data with some (unrealistically) large effect sizes (many OR>2).

tobyjohnson/gtx documentation built on Aug. 30, 2019, 8:07 p.m.