Question

Shivani

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Shivani • 0

@3bb25ffc

Last seen 2.0 years ago

Israel

Hi, I am trying to find out the pathways through Pathfinder(KEGG) but everytime this problem is poping up. I aslo updated the version ofR , one time it ran but gain the same problem. Please help me...

RA_output4 <- run_pathfindR(RA_input4, max_to_plot = NULL)


sessionInfo( )
Downloading pathway diagrams of 174 KEGG pathways

  |=================                                                                                       |  17%The file /var/folders/k3/2bypsbdn7mgb7n3gt5q6jhhc0000gn/T//RtmpdZPOY3/file5f11d81aca8 seems not to be a valid KGML file

Detailed error messages fromXML::xmlTreeParse:
Error: 1: Couldn't find end of Start Tag rela line 1374
2: Premature end of data in tag pathway line 4
> library(pathfindR)

kegg • 892 views

ADD COMMENT • link updated 2.1 years ago by deeenes ▴ 60 • written 2.1 years ago by Shivani • 0

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pathfindR is a CRAN package not a Bioconductor package and the maintainers are not required to be on this mailing list. You might consider placing on stackoverflow.

ADD REPLY • link 2.1 years ago shepherl 4.1k

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To access KEGG Pathways you can also try this: https://saezlab.github.io/OmnipathR/reference/kegg_pathways_download.html
More pathway data (directed and signed signalling network) is available by https://saezlab.github.io/OmnipathR/reference/import_omnipath_interactions.html
To find paths in a network this is one option: https://saezlab.github.io/OmnipathR/reference/find_all_paths.html (I haven't checked what the function in your post does, I just associated by its name, sorry if not relevant)

ADD REPLY • link 2.1 years ago deeenes ▴ 60