RIVER: RIVER: R package for an implementation of an extensible...
In ipw012/RIVER: R package for RIVER (RNA-Informed Variant Effect on Regulation)
Description
getFuncRvFeat
getFuncRvPosteriors
mleBeta
mleTheta
testPosteriors
integratedEM
plotPosteriors
evalRIVER
appRIVER
Source
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
ipw012/RIVER documentation built on March 8, 2020, 7:54 p.m.
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Description getFuncRvFeat getFuncRvPosteriors mleBeta mleTheta testPosteriors integratedEM plotPosteriors evalRIVER appRIVER Source
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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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