RIVER {RIVER} | R Documentation

## RIVER: R package for an implementation of an extensible predictive model for combining whole genome sequences with molecular phenotypes to identify high-impact rare variants.

### Description

The RIVER package provides two applicable functions of RIVER to actual datasets including genomic features and outlier status and a list of required functions for RIVER: evalRIVER, appRIVER, getFRPosteriors, mleTheta, mleBeta, getFRgivenG, testPosteriors, and integratedEM.

### getFuncRvFeat

The `getFuncRvFeat` computes posterior probabilities of FR (functionality of regulatory variant) given genomic features (G) and current estimate of beta (parameters between FR and G).

### getFuncRvPosteriors

The `getFuncRvPosteriors` computes posterior probabilities of FR (functionality of regulatory variant) given genomic features (G) and outlier status (E) with current estimate of beta (parameters between FR and G) and theta (parameters between FR and E).

### mleBeta

The `mleBeta` computes maximum likelihoood estimate of beta (parameters between FR and G; multivariate logistic regression).

### mleTheta

The `mleTheta` computes maximum likelihoood estimate of theta (parameters between FR and E; Naive-Bayes).

### testPosteriors

The `testPosteriors` computes posterior probabilities of FR (functionality of regulatory variant) given G (genomic annotations) and E (outlier status) with estimate of beta (parameters between FR and G) and theta (parameters between FR and E).

### integratedEM

The `integratedEM` iteratively executes e-step and m-step until it converges. This is a main function of RIVER.

### plotPosteriors

The `plotPosteriors` draw scatter plots of posterior probabilities from both RIVER GAM in terms of outliers status.

### evalRIVER

The `evaRIVER` trains RIVER by holding out a list of individual and gene pairs having same rare variants for evaluation, computes test posterior probabilities of FR (functionality of regulatory variant) for 1st individual, and compares them with outlier status of 2nd individual from the list.

### appRIVER

The `appRIVER` trains RIVER with all instances and computes posterior probabilities of FR (functionality of regulatory variant) for downstream analyses.

### Source

https://github.com/ipw012/RIVER

[Package RIVER version 1.11.0 Index]