I want to kindly ask how can we run Reactome for run_pathfindR for mouse (Mus musculus) genes?
I have never used PathFindR, but from looking at the tutorial here: Enrichment Analysis, Clustering and Scoring with pathfindR
It looks like you need to provide the output of an RNA-seq comparison generated from DESeq2 or other DGE analysis package (EdgeR?). Check out the tutorial I linked above...
If you can see... the input for PathFindR looks something like this:
Gene.symbol logFC adj.P.Val
1 FAM110A -0.69394 3.4087e-06
2 RNASE2 1.35350 1.0085e-05
3 S100A8 1.54483 3.4664e-05
4 S100A9 1.02809 2.2626e-04
5 TEX261 -0.32360 2.2626e-04
6 ARHGAP17 -0.69193 2.7081e-04
This would be the standard output of DESeq2 (except that logFC would be log2FC). Maybe someone else could chime in here as well, with regard to using LogFC or Log2FC?
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