computeDS {TNBC.CMS} | R Documentation |
Computes drug signature scores. Also draws heatmap representing the average signature scores for each subtype.
computeDS(expr, pred, gene.set = NULL)
expr |
A |
pred |
A vector of predicted consensus molecular subtypes. |
gene.set |
A user-provided list of gene sets associated with drug response. Names of gene sets must follow the format of [DRUG NAME]_[RESISTANCE/RESPONSE]_[UP/DN] (e.g. CISPLATIN_RESISTANCE_DN). |
Drug signature scores are the average of expression values of genes included in gene sets from MSigDB.
A matrix of drug signature scores.
Liberzon, A. et al. (2011). Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27, 1739-40.
# Load gene expression profiles of TNBC samples data(GSE25055) # Predict consensus molecular subtypes of TNBC samples prediction <- predictCMS(expr = GSE25055) # Compute drug signature scores resultDS <- computeDS(expr = GSE25055, pred = prediction)