performGSVA {TNBC.CMS} | R Documentation

## Gene set variation analysis

### Description

Performs GSVA on gene sets. Also draws a heatmap representing GSVA scores.

### Usage

    performGSVA(expr, pred, gene.set = NULL, gsva.kcdf = "Gaussian")

### 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` | Gene sets provided as a list. If NULL, the hallmark pathway gene sets are used.
`gsva.kcdf` | Kernel to be used in the estimation of the cumulative distribution function. By default, this is set to `"Gaussian"` which is suitable for continuous expression values. If expression values are counts, `"Poisson"` is recommended.

### Details

This is a wrapper function of the `gsva` function in the `GSVA` package to compute GSVA enrichment scores per sample and produce a heatmap comparing them across consensus molecular subtypes.

### Value

A matrix of GSVA enrichment scores.

### References

Liberzon, A. et al. (2015). The molecular signatures database hallmark gene set collection. Cell systems, 1, 417-425.

### Examples

    # Load gene expression profiles of TNBC samples
    data(GSE25055)

    # Predict consensus molecular subtypes of TNBC samples
    prediction <- predictCMS(expr = GSE25055)

    # Perform GSVA on the hallmark pathway gene sets
    resultGSVA <- performGSVA(expr = GSE25055, pred = prediction)

[Package TNBC.CMS version 1.4.0 Index]