bimetallic-package: Power for SNP analyses using silver standard cases

In bimetallic: Power for SNP analyses using silver standard cases

Description

A power calculator for Genome-wide association studies (GWAs) with combined gold (error-free) and silver (erroneous) phenotyping per McDavid A, Crane PK, Newton KM, Crosslin DR, et al. (2011)

Details

Package:	bimetallic
Type:	Package
Version:	1.0
Date:	2011-08-03
License:	GPL-2
LazyLoad:	yes

chisq.sim.factory, chisq.lytic.func and dlambda, is.legal all use common parameters. chisq.sim.factory returns a function that repeatedly calculates chi-square statistics (X^2) and point estimates of allelic odds ratios (allelicOR) for a study specified by the simulation parameters. chisq.lytic.func returns lambda, the non-centrality parameter of the asymptotic sampling distribution of (X^2), which happens to be non-central chi-square with two degrees of freedom. dlambda returns the derivative of lambda with respect to gam_ca or gam_co. If this is positive then power is increasing with the addition of a silver-standard subject. is.legal determines if the parameters provided are ‘legal’ in the sense of inducing valid probabilities in affected and unaffected populations in the simulation

Author(s)

Andrew McDavid

Maintainer: Andrew McDavid <[e-mail]>

References

See McDavid A, Crane PK, Newton KM, Crosslin DR, et al. (2011) for a full description of the model and parameters.

Examples

##Make a chisq simulator under a study scenario
sim = chisq.sim.factory(R = 4, gam_ca = 3, gam_co = 0,
	ppv = .8, npv = 1, homRR = 2.2, N_co = 1000,
	maf = .1, prev = .01, model = "mult")

##Run one realization of the simulation
sim()

bimetallic documentation built on May 2, 2019, 1:27 p.m.