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SimReg (version 3.3)

Similarity Regression

Description

Similarity regression, evaluating the probability of association between sets of ontological terms and binary response vector. A no-association model is compared with one in which the log odds of a true response is linked to the semantic similarity between terms and a latent characteristic ontological profile - 'Phenotype Similarity Regression for Identifying the Genetic Determinants of Rare Diseases', Greene et al 2016 .

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Version

Install

install.packages('SimReg')

Monthly Downloads

285

Version

3.3

License

GPL (>= 2)

Maintainer

Daniel Greene

Last Published

February 15th, 2021

Functions in SimReg (3.3)

print.sim_reg_summary

Print sim_reg_summary object
plot_term_marginals

Create ontological plot of marginal probabilities of terms
get_term_marginals

Calculate marginal probability of terms inclusion in phi from sim_reg_out object
SimReg3-package

Similarity Regression Functions
posterior_prediction

Predicted probability of y given x conditional on association and given data.
term_marginals

Calculate marginal probability of terms inclusion in phi
summary.sim_reg_output

Get summary of sim_reg_output object
print.sim_reg_output

Print sim_reg_output object
prob_association

Calculate probability of association between y and x
sim_reg

Similarity regression
sum_log_probs

Calculate sum of log probabilities on log scale without over/under-flow
plot.sim_reg_summary

Plot summary of sim_reg_output object
get_terms

Get full set of terms to use in inference procedure based on similarity function arguments
log_BF

Calculate log Bayes factor for similarity the model, gamma=1 and baseline model, gamma=0.