R package for RIVER (RNA-Informed Variant Effect on Regulation)


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Documentation for package ‘RIVER’ version 1.11.0

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RIVER-package 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.
appRIVER Application of RIVER
evaRIVER Evaluation of RIVER
getData Get coordinated data from a compressed file for RIVER
getFuncRvFeat Posterior probabilities of FR given G
getFuncRvPosteriors Posterior probabilities of FR given G and E.
integratedEM An iterative expectation-maximization algorithm for RIVER
mleBeta Maximum likelihoood estimate of beta.
mleTheta Maximum likelihoood estimate of theta.
plotPosteriors Draw scatter plots of posterior probabilities from both RIVER GAM in terms of outlier status.
RIVER 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.
testPosteriors Test posterior probabilities of FR given G and E