Assign gene signature in other cohort

Question

[sunnlife]

Hi,

Via a GSE dataset, I identify a gene signature of hundred of genes specific to a particular class of samples. Now I want identify another samples (from a distinct cohort) who upregulated my homemade signature. How can i do this in R ? or in another language ? Thanks in advance

Alex

Answer 1

[rpolicastro]

In R you can take your custom signature and make a two column data.frame with columns 'term' and 'gene', and then pass it to the TERM2GENE argument of the GSEA function from clusterProfiler.