thyroidBRS - BRAF-RAS Score (BRS) Classifier for Papillary Thyroid Carcinoma

Computes the BRAF-RAS Score (BRS), a 71-gene expression-based signature that quantifies whether a papillary thyroid carcinoma (PTC) sample resembles a BRAF-V600E-mutant or a RAS-mutant transcriptional profile, following Agrawal et al. (2014) <doi:10.1016/j.cell.2014.09.050>, Extended Experimental Procedures, section 14.1. It is a re-implementation from that description rather than the original code, which was never released: it reproduces the published classification (99.7 percent against driver-mutation status under cross-validation) but not the exact published score values. The original study only scored the subset of samples for which both exome and RNA sequencing data were available, since exome data was needed to define the two reference groups (but not to score additional samples). This package lets you fit the reference centroids from any cohort with known BRAF-mutant/RAS-mutant labels and then score new samples — including ones with expression data only — using just their gene expression. Expression can be supplied as a matrix, a SummarizedExperiment or an ExpressionSet.