getFuncRvFeat {RIVER} | R Documentation |
getFuncRvFeat
computes posterior probabilities of FR (functionality of
regulatory variant) given G (genomic features) and current estimate
of beta (parameters between FR and G).
getFuncRvFeat(Feat, logistic.model, lambda)
Feat |
Genomic features (G) |
logistic.model |
Logistic regression model with current estimate of beta |
lambda |
Selected lambda |
probabilities of FR given genomic features, P(FR | G)
Yungil Kim, ipw012@gmail.com
dataInput <- getData(filename=system.file("extdata", "simulation_RIVER.gz", package = "RIVER"), ZscoreThrd=1.5) Feat <- scale(t(Biobase::exprs(dataInput))) # genomic features (G) Out <- as.vector(as.numeric(unlist(dataInput$Outlier))-1) # outlier status (E) costs <- c(100, 10, 1, .1, .01, 1e-3, 1e-4) logisticAllCV <- glmnet::cv.glmnet(Feat, Out, lambda=costs, family="binomial", alpha = 0, nfolds=10) probFuncRvFeat <- getFuncRvFeat(Feat, logistic.model=logisticAllCV$glmnet.fit, lambda=logisticAllCV$lambda.min)