plot.gseaSignatures: GSEA-like Plot.

In phenoTest: Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.

Description

Builds a GSEA plot using a gseaSignature object (one of gseaSignaturesSign or gseaSignaturesVar obtained with the gseaSignatures function) and a gseaSignificance object (one of gseaSignificanceSign or gseaSignificanceVar obtained with the gseaSignificance function).

Usage

plot.gseaSignaturesSign(x,gseaSignificance,es.ylim,nes.ylim,es.nes="both",...)

Arguments

x	object of class gseaSignaturesSign or gseaSignaturesVar.
gseaSignificance	object of class gseaSignificanceSign or gseaSignificanceVar.
es.ylim	ylim values for the ES plot.
nes.ylim	ylim values for the NES plot.
es.nes	can be "es" if we want to plot enrichment score, "nes" if we want to plot normalised enrichment scores or "both"if we want to plot them both.
...	Arguments to be passed to plot.

Author(s)

Evarist Planet

References

Aravind Subramanian, (October 25, 2005) Gene Set Enrichment Analysis. www.pnas.org/cgi/doi/10.1073/pnas.0506580102

See Also

plot.gseaSignaturesSign, plot.gseaSignaturesVar

Examples

#for examples see the help file of gseaSigntaures: ?gseaSignatures

phenoTest documentation built on Nov. 8, 2020, 7:53 p.m.