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