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23 months ago by

Hello:

I have a list of Kegg Orthology (K) numbers that I would like to covert from K to entrezID to use clusterProfiler package. Currently, I am trying to install the package org.Hs.egPATH to use with the bitr command from clusterProfiler. My inquiry is this:

I am getting the following error after I run the following command: source("https://bioconductor.org/biocLite.R")
biocLite("org.Hs.egPATH”)

1: package ‘org.Hs.egPATH’ is not available (for R version 3.3.1)

2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
installation of package ‘Matrix’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
installation of package ‘rgl’ had non-zero exit status

I was able to download the org.Hs.eg.db package without a problem. Any recommendations as to when it will be available? Is there a work-around on how to obtain the org.Hs.egPATH package?

Thank you very much!

Joany

modified 22 months ago by Guangchuang Yu1.0k • written 23 months ago by ladypurrsia0

Thank you so very much, Martin!

Joany

pls tag the post with clusterprofiler.

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23 months ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

'org.Hs.egPATH' is not a package, but a variable in the org.Hs.eg.db package, so

biocLite("org.Hs.eg.db")
library(org.Hs.eg.db)
org.Hs.egPATH

but unfortunately the information in this object is now several years old (KEGG no longer freely distributes the aggregate information. You might try the KEGGREST package instead.

Is the KEGGREST package needed? It seems to me that one can read the info directly from the KEGG website without needing an intermediary package:

EG.KEGG <- read.table("http://rest.kegg.jp/link/pathway/hsa",stringsAsFactors=FALSE)
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22 months ago by
Gordon Smyth34k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth34k wrote:

You can read the latest Entrez ID to KEGG links from the following URL at any time:

The getGeneKEGGLinks() function in the limma package automates this for you:

> library(limma)
GeneID     PathwayID
1  10327 path:hsa00010
2    124 path:hsa00010
3    125 path:hsa00010
4    126 path:hsa00010
5    127 path:hsa00010
6    128 path:hsa00010

The first column in Entrez ID and the second is KEGG pathway ID.

However I rather doubt that you need to do any ID conversion to use the clusterProfiler package. I'm pretty sure that the clusterProfiler package knows how to access the KEGG website and that it works fine with Entrez IDs. The bitr() function is intended to convert between gene ID systems, not between gene IDs and pathway IDs. If you have Entrez IDs then you're already ready to go, because KEGG is Entrez Id based.

He doesn't have entrezgene ID and only have a list of K number (very curious and I also have no idea).

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22 months ago by
Guangchuang Yu1.0k
Hong Kong
Guangchuang Yu1.0k wrote:

1. bitr doesn't support converting K number to gene ID.

2. You can use enrichKEGG with a list of K number as input gene, see also #clusterProfiler# KEGG enrichment with non-reference species