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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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how to use pathfindR for mouse data? #4

Closed steffenheyne closed 6 years ago

steffenheyne commented 6 years ago

Hi, I would like to use your package for mouse data? It seems all is fixed to human gene symbols etc.

Would it be possible to replace the appropriate objects like pathfindR::reactome_genes pathfindR::kegg_pathways

with the mouse versions and the proceed as usual?

I think you should provide at least the option to use also mouse in addition to human! thanks, steffen

egeulgen commented 6 years ago

Hey, if you can do so, replacing the objects kegg_genes and kegg_pathways should work. The package was conceived with human applications as a priority but you're absolutely right, I'll try to add the option to use mouse PIN and KEGG pathways in the next release.

egeulgen commented 6 years ago

Hello again,

To keep the package size small, we'll only keep the current (human) PINs and gene sets for now. I do have a fix for your problem though:

There was already the option to specify a custom PIN. I've just implemented the option to specify a custom gene set. 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.

This makes it possible to replace the default gene set data.

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

Hope it's helpful, Best, -E

steffenheyne commented 6 years ago

thanks, I'll try! Regarding general support of other organisms, there are some R/Bioconductor packages like Biomart or AnnotationDbi etc that can be used to convert Human EntrezIDs eg for MSigDB. KEGG already has some interface and package to download organsim specific versions of KEGG pathways.

egeulgen commented 5 years ago

vignette for non-human organisms

shehroz-m commented 5 years ago

hey @steffenheyne have you had any success with using pathfindR with mouse data? If so, I would be glad to know how you managed!

thanks, Shehroz