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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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pathfindR mouse #5

Closed rvaldes closed 6 years ago

rvaldes commented 6 years ago

Is there any possibility to run pathfindR for mouse data?

Thanks

Rafa

egeulgen commented 6 years ago

hey Rafa,

There was already the option to specify a custom PIN and as of the latest development version, there is an option to specify custom gene sets. For this, you should:

  1. Set the gene_sets argument to "Custom"
  2. To the custom_genes argument, provide a list object whose names are pathway IDs and elements are vectors of gene symbols contained in that pathway.
  3. To the custom_pathways argument, provide a named vector of pathway names, the names of the vector here are pathway IDs.

You can use this feature with the latest development version. See here for installation of the development version.

Best, -E

egeulgen commented 5 years ago

vignette for non-human organisms