computeDS {TNBC.CMS} | R Documentation

## Computation of drug signature scores.

### 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)

[Package TNBC.CMS version 1.4.0 Index]