igsva {GSVA} | R Documentation

## Gene Set Variation Analysis

### Description

Starts an interactive GSVA shiny web app.

### Usage

    igsva()

### Details

GSVA assesses the relative enrichment of gene sets across samples using a non-parametric approach. Conceptually, GSVA transforms a p-gene by n-sample gene expression matrix into a g-geneset by n-sample pathway enrichment matrix. This facilitates many forms of statistical analysis in the 'space' of pathways rather than genes, providing a higher level of interpretability.

The `igsva()` function starts an interactive shiny web app that allows the user to configure the arguments of the `gsva()` function and runs it on the computer. Please see the manual page of the `gsva()` function for a description of the arguments and their default and alternative values.

The input data may be loaded from the users workspace or by selecting a CSV file for the expression data, and a GMT file for the gene sets data.

### Value

A gene-set by sample matrix of GSVA enrichment scores after pressing the button 'Save & Close'. This result can be also downloaded as a CSV file with the 'Download' button.

### Author(s)

J. Fernández and R. Castelo

### References

Hänzelmann, S., Castelo, R. and Guinney, J. GSVA: Gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics, 14:7, 2013.

### See Also

`gsva`

### Examples

    ## Not run:
    res <- igsva() ## this will open your browser with the GSVA shiny web app

    ## End(Not run)

[Package GSVA version 1.38.2 Index]