iFad-package
(Package: iFad) :
An integrative factor analysis model for drug-pathway association inference
This package implements a bayesian sparse factor model for the joint analysis of paired datasets, one is the gene expression dataset and the other is the drug sensitivity profiles, measured across the same panel of samples, e.g., cell lines. Prior knowledge about gene-pathway associations can be easily incorporated in the model to aid the inference of drug-pathway associations.
● Data Source:
CranContrib
● Keywords:
● Alias: iFad, iFad-package
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data_simulation
(Package: iFad) :
Simulation of example dataset for the factor analysis model
Simulation of gene expression data, drug sensitivity data, as well as gene-pathway association matrix
● Data Source:
CranContrib
● Keywords:
● Alias: data_simulation
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ROC_plot
(Package: iFad) :
Calculate the AUC (area under curve) and generate ROC plot
This function evaluates the inference performance of the sparse factor analysis model by using different cut-off values to calculate the sensitivity and specificity of the result of the Gibbs sampling algorithm. In this way, it can give the AUC (area under curve) value and plot the receiver-operating-curve.
● Data Source:
CranContrib
● Keywords:
● Alias: ROC_plot
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mcmc_trace_plot
(Package: iFad) :
Traceplot of the Gibbs sampling iterations
Plot the updated standard deviation of gene in every recorded Gibbs sampling iteration
● Data Source:
CranContrib
● Keywords:
● Alias: mcmc_trace_plot
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gibbs_sampling
(Package: iFad) :
Gibbs sampling for the inference of the inference of
This function implements the collapsed Gibbs sampling algorithm for the inference of unknown parameters in the proposed sparse factor analysis model
● Data Source:
CranContrib
● Keywords:
● Alias: gibbs_sampling
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Ymean_compare
(Package: iFad) :
Compare the infered Y_mean values with the true values
Calculate the RMSE (root-mean-sqaured-error) of the inferred mean of matrixY1 and matrixY2 compared with the original true means of matrixY1 and Y2
● Data Source:
CranContrib
● Keywords:
● Alias: Ymean_compare
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