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Question: Cannot download org.Hs.egPATH
0
gravatar for ladypurrsia
14 months ago by
ladypurrsia0 wrote:

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 

ADD COMMENTlink modified 14 months ago by Guangchuang Yu800 • written 14 months ago by ladypurrsia0

Thank you so very much, Martin!

Joany

ADD REPLYlink written 14 months ago by ladypurrsia0

pls tag the post with clusterprofiler.
 

ADD REPLYlink written 14 months ago by Guangchuang Yu800
1
gravatar for Martin Morgan
14 months ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k 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.

ADD COMMENTlink written 14 months ago by Martin Morgan ♦♦ 20k

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)
ADD REPLYlink modified 14 months ago • written 14 months ago by Gordon Smyth32k
1
gravatar for Gordon Smyth
14 months ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

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

  http://rest.kegg.jp/link/pathway/hsa

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

> library(limma)
> EG.KEGG <- getGeneKEGGLinks("hsa")
> head(EG.KEGG)
  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.

ADD COMMENTlink modified 14 months ago • written 14 months ago by Gordon Smyth32k

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

ADD REPLYlink modified 14 months ago • written 14 months ago by Guangchuang Yu800
0
gravatar for Guangchuang Yu
14 months ago by
Hong Kong
Guangchuang Yu800 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

 

ADD COMMENTlink written 14 months ago by Guangchuang Yu800
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