Description Details Author(s) References Examples
HMVD performs an association test between a group of variables and the outcome. Posterior probabilities are provided for each variable indicating how likely each variable is associated with the outcome.
Package: | HMVD |
Type: | Package |
Version: | 1.0 |
Date: | 2016-05-12 |
License: | GPL-3 |
~~ An overview of how to use the package, including the most important functions ~~
Maintainer: Yichen Cheng<ycheng@fredhutch.org>
Cheng, Y., Dai, J. and Kooperberg, C. (2015). Group association test using hidden Markov model. Biostatistics, in pres.
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#### compute the p-value and do parameter estimation for continuous outcome
n = 4000; m = 20
X = matrix(rnorm(n*m),n)
Y = rowMeans(X[,1:4])*.2 + rnorm(n)
HMVD(Y,X)$p.value #### approximate p-value
HMVD(Y,X,nperm.max = 20)$p.value.perm #### p-value based on permutations
#### in practice we would use more permutations
out = HMVD(Y,X,method='estimation')
round(out$prob,2) ###posterior probability
out$theta ### common effect size
#### compute the p-value and do parameter estimation for binary outcome
n = 4000; m = 20
X = matrix(rnorm(n*m),n)
p = rowMeans(X[,1:4])*.4
Y = rbinom(n,1,p = exp(p)/(1+exp(p)))
HMVD(Y,X,model.type='D')$p.value #### approximate p-value
HMVD(Y,X,nperm.max = 20)$p.value.perm #### p-value based on permutations
#### in practice we would use more permutations
out = HMVD(Y,X,model.type='D',method='estimation')
round(out$prob,2) ###posterior probability
out$theta ### common effect size
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