Description Details Author(s) References Examples
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)
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
Andrew McDavid
Maintainer: Andrew McDavid <amcdavid@fhcrc.org>
See McDavid A, Crane PK, Newton KM, Crosslin DR, et al. (2011) for a full description of the model and parameters.
1 2 3 4 5 6 7 | ##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()
|
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