ASSIGN Functions

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

GFRN Functions

ComBat.step2

Perform the second step of ComBat

optimizeGFRN

Optimize GFRN gene lists lengths

runassignGFRN

Run optimized single pathway ASSIGN

Data

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)

Helpers

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