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.
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
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.
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.
J. Fernández and R. Castelo
Hänzelmann, S., Castelo, R. and Guinney, J. GSVA: Gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics, 14:7, 2013.
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## Not run: res <- igsva() ## this will open your browser with the GSVA shiny web app ## End(Not run)
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