mthfrex: Simulated example finemapping genotype and phenotype data.
Description
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.
Format
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.Source
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).Details
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.