Introduction to the ASSIGN Package

This vignette provides an overview of the Bioconductor package ASSIGN for signaturebased profiling of heterogeneous biological pathways. ASSIGN (Adaptive Signature Selection and InteGratioN) is a computational tool to evaluate the pathway deregulation/activation status in individual patient samples. ASSIGN employs a flexible Bayesian factor analysis approach that adapts predetermined pathway signatures derived either from knowledge-based literatures or from perturbation experiments to the cell/tissue-specific pathway signatures. The deregulation/activation level of each contextspecific pathway is quantified to a score, which represents the extent to which a patient sample encompasses the pathway deregulation/activation signature. Some distinguishable features of ASSIGN are described as follows: 1). multiple