To order list of genes

Question

[rufusek500]

Hello, I obtained my list of genes after DESeq2 and I want to order my list of genes based on up and downregulation. Do you recommend me any command or pacakge which enables me to order my list of genes?

[Marco Pannone]

If, let's say, you stored your full list of DEGs in a variable called res, you can simply do so:

#for UP DEGs with logFC threshold >= 1 and significant at adjusted p-value <= 0.05
degenes_up <- subset(res, res$padj <= 0.05 & res$log2FoldChange >= 1)

#for DOWN DEGs with logFC threshold <= -1 and significant at adjusted p-value <= 0.05
degenes_down <- subset(res, res$padj <= 0.05 & res$log2FoldChange <= -1)

Naturally, adjust the logFC threshold based on your preferences.

[rufusek500]

Thanks for the answear, it worked!

[Matthias Zepper]

Ironically, this command is called order:

data(mtcars)
mtcars[order(mtcars$qsec),]

See ?order for details.

Answer 1

[benformatics]

i would just drop any with an adjusted p-value below some threshold (depending on how many DGE I have) then sort based on log2FC.

just do it in R:subset(dge[order(dge$log2FC, decreasing=TRUE),],p.adjust <= 0.5) for up-reg etc...