computeDS: Computation of drug signature scores.

In TNBC.CMS: TNBC.CMS: Prediction of TNBC Consensus Molecular Subtypes

Description

Computes drug signature scores. Also draws heatmap representing the average signature scores for each subtype.

Usage

computeDS(expr, pred, gene.set = NULL)

Arguments

expr	A SummarizedExperiment object or a matrix containig gene expression profiles. If input is a SummarizedExperiment, the first element in the assays list should be a matrix of gene expression. Rows and columns of the gene expression matrix correspond to genes and samples, respectively (rownames must be to gene symbols).
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).

Details

Drug signature scores are the average of expression values of genes included in gene sets from MSigDB.

Value

A matrix of drug signature scores.

References

Liberzon, A. et al. (2011). Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27, 1739-40.

Examples

# 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)

TNBC.CMS documentation built on Nov. 8, 2020, 7:53 p.m.