igsva: Gene Set Variation Analysis

In rcastelo/GSVA: Gene Set Variation Analysis for Microarray and RNA-Seq Data

Gene Set Variation Analysis

Description

Starts an interactive GSVA shiny web app.

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.

Usage

igsva()

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)

rcastelo/GSVA documentation built on April 19, 2024, 10:10 a.m.