In sidiropoulos/PSigA: A gene-signature ranking method based on sample density in PCA space

PSigA Output Report

This is a minimal example of using knitr to produce an HTML page from Markdown.

GSEA

library(PsigA)

plot(prcomp(t(data), scale = scale)$x, pch = 20, cex = .8)

PC1

rownames(gsea$pc1) <- gsub("\\(|\\)","", rownames(gsea$pc1))
kable(head(gsea$pc1, escape = TRUE, n = 10))

PC2

rownames(gsea$pc2) <- gsub("\\(|\\)","", rownames(gsea$pc2))
kable(head(gsea$pc2, escape = TRUE, n = 10))

Top scoring signatures

topSignatures <- rownames(scores)[1:10]
for (i in topSignatures){
    print(sigBiplot(data, signatures[[i]], main = i))
}

sidiropoulos/PSigA documentation built on May 29, 2019, 9:58 p.m.