Main ASSIGN functions for prediction.
assign.convergence()
Check the convergence of the MCMC chain
assign.cv.output()
Cross validation output
assign.mcmc()
The Gibbs sampling algorithm to approximate the joint distribution of the model parameters
assign.output()
Prediction/validation output for test data
assign.preprocess()
Input data preprocessing
assign.summary()
Summary of the model parameters estimated by the Gibbs sampling algorithm
assign.wrapper()
ASSIGN All-in-one function
ComBat.step2()
Perform the second step of ComBat
optimizeGFRN()
Optimize GFRN gene lists lengths
runassignGFRN()
Run optimized single pathway ASSIGN
excludegenes
Exclude Gene List
geneList1
Pathway signature gene sets
gfrn_geneList
Pathway Signature Gene Lists
testData1
Gene expression profiling from cancer patients (test dataset)
trainingData1
Gene expression profiling from cell line perturbation experiments (training dataset)
gather_assign_results()
Gather the ASSIGN results in a specific directory
merge_drop()
Combine two data frames
pcaplot()
Display a PCA Plot of the Data