Question: Geseca output, column "size"

[oswaldbra12]

Hello,

Thank you for this. I think I have a simple question but can't seem to figure it out. One of the outputs of geseca is a data frame. In that data frame there is a "size" column. There is a number associated with the pathways analyzed. Are those the gene hits and if so, how can I pull those hits for my reference?

Example:

Thanks.

[assaron]

Hi @oswaldbra12

size column has the same meaning as in fgsea(): it's the effective number of genes in the gen set, that is the size of intersection of the gene set and all of the genes in the input matrix. You can get these genes by doing the same intersection yourself.

Hope that helps.

[oswaldbra12]

Thank you for the quick comment @assaron,

I figured that might be the case. I am having some trouble parsing out what those genes are in each geneset. Do you by chance have time to elaborate on how I can get those genes. For example: the best way to grab the 33 gene names from row number "4" in the screenshot above?

I'm just struggling with it a bit.

[assaron]

Something like this should work: unique(intersect(pathways[["NAME_OF_THE_PATHWAY"]], rownames(E))), assuming pathways is your list of pathways, E is the input expression matrix and NAME_OF_THE_PATHWAY is the name of the pathway you are interested in (I can't see it from the screenshot)

[oswaldbra12]

This worked great. Thank you for helping me with this. Much appreciated!