Im using this code to make based on log2foldchange and padj value ,im getting the plot but i want those value for my reference how do i extract the same .
alpha <- 0.05 # Threshold on the adjusted p-value
cols <- densCols(res$log2FoldChange, -log10(res$pvalue))
plot(res$log2FoldChange, -log10(res$padj), col=cols, panel.first=grid(),
main="Volcano plot", xlab="Effect size: log2(fold-change)", ylab="-log10(adjusted p-value)",
pch=20, cex=0.6)
abline(v=0)
abline(v=c(-1,1), col="brown")
abline(h=-log10(alpha), col="brown")
gn.selected <- abs(res$log2FoldChange) > 2.5 & res$padj < alpha
text(res$log2FoldChange[gn.selected],
-log10(res$padj)[gn.selected],
lab=rownames(res)[gn.selected ], cex=0.4)
when i view gn.selected i get only logical value that is true or false
Any help or suggestion would be highly appreciated
Update I'm doing this
> DF <- DF[DF$log2FoldChange > 1.5 & DF$padj < 0.05,]
is that suffice and am i doing it correctly ?