How to bring own custom background to gseapy

[Cher-HAN]

Hi zq,

Thanks so much for the useful package and congratulations to the gseapy paper.
I am doing an analysis of GO terms, and there are no significant enriched GO terms, and I guess it is because the default background(whole human protein-coding genes) includes many irrelevant GO terms.
I could use a biological meaningful condition to filter the background annotation, and I plan to generate my own gmt annotation and then supply the gmt file to gseapy as custom background.
However, I am curious whether I could input a list of gene names to gseapy, and it could automatically generate the custom background base on the gene list.

Kind regards,
Xueer

[zqfang]

What function you'er trying to use ?

if gseapy.enrich() or gseapy.enrichr(). Just set the background argument to your own input gene list

see some explanation here

[Cher-HAN]

I am using prerank.

[zqfang]

the background is your input ranking list for gsea, prerank, ssgsea

[Cher-HAN]

I think the background is "gene_sets". And is it possible that I input a list of genes to generate the custom a gene_sets?

[zqfang]

Of course. All you need is given gene_sets a dict or GMT file your own.

check this tutorial out