KEGG Pathway in R
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salethlr • 0
@e2e9367f
Last seen 9 weeks ago
Canada

Hi, I am a beginner trying to do RNA Seq in R and currently facing issues while trying to do KEGG Pathway analysis. I am using the recent version of R Studio (4.2.0) After running the tmp command, it appears that the pathway doesn't exsist. Out of the 5, I have got I pathway and not the rest. It would really great if you can help me out.

>keggresids
[1] "hsa04614" "hsa04142" "hsa04145" "hsa04141" "hsa00980"
> tmp=sapply(keggresids,function(pid)pathview(gene.data=foldchanges,pathway.id=pid,species="hsa"))
Info: Downloading xml files for hsa04614, 1/1 pathways..
Warning: Download of hsa04614 xml file failed!
This pathway may not exist!
Info: Downloading png files for hsa04614, 1/1 pathways..
Warning: Download of hsa04614 png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa04614 skipped!
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory C:/Users/leena/OneDrive/Desktop/RNA Seq-TaMXene-Weiang-May2022
Info: Writing image file hsa04142.pathview.png
Info: some node width is different from others, and hence adjusted!
Info: Downloading xml files for hsa04145, 1/1 pathways..
Warning: Download of hsa04145 xml file failed!
This pathway may not exist!
Info: Downloading png files for hsa04145, 1/1 pathways..
Warning: Download of hsa04145 png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa04145 skipped!
Couldn't find end of Start Tag relation line 704
Premature end of data in tag pathway line 4
Warning: Parsing ./hsa04141.xml file failed, please check the file!
Info: Downloading xml files for hsa00980, 1/1 pathways..
Warning: Download of hsa00980 xml file failed!
This pathway may not exist!
Info: Downloading png files for hsa00980, 1/1 pathways..
Warning: Download of hsa00980 png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa00980 skipped!
Warning messages:
1: In download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa04614/kgml': status was 'Failure when receiving data from the peer'
2: In download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa04145/kgml': status was 'Failure when receiving data from the peer'
3: In download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa00980/kgml': status was 'Failure when receiving data from the peer'
keggrespathways KEGG • 1.0k views
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