[BioC] R: R: Pathway Information

Fri Jun 17 12:58:54 CEST 2005

Now it works!

get(paste("hsa", get("Biosynthesis of steroids", KEGGPATHNAME2ID),sep=
""),KEGGPATHID2EXTID)
 [1] "10654" "10682" "1717"  "1728"  "2222"  "2224"  "3156"  "3422"
"4047"  "4597"  "4598"  "4835"  "51302" "6309"  "6713"  "79001" "91734"
"9420"  "9453"

but if now i would like to create a file ex CVS in which i can have:

"10654" ----> pathway1.....
"10682"-----> pathway2

"9420"------->pathwayN

how can i obtain it?

thanks

-----Messaggio originale-----
Da: John Zhang [mailto:jzhang at jimmy.harvard.edu] 
Inviato: giovedì 16 giugno 2005 17.56
A: jzhang at jimmy.harvard.edu; michael.auer at meduniwien.ac.at;
rhaddad at genetics.wayne.edu; alberto.goldoni at eurogene.org
Cc: bioconductor at stat.math.ethz.ch
Oggetto: Re: R: [BioC] Pathway Information

Sorry for the typo. steriods should be steroids.

>X-Original-To: jzhang at jimmy.harvard.edu
>Delivered-To: jzhang at jimmy.harvard.edu
>From: "Alberto Goldoni" <alberto.goldoni at eurogene.org>
>To: "'John Zhang'" <jzhang at jimmy.harvard.edu>,
<michael.auer at meduniwien.ac.at>, 
<rhaddad at genetics.wayne.edu>
>Cc: <bioconductor at stat.math.ethz.ch>
>Subject: R: [BioC] Pathway Information
>Date: Thu, 16 Jun 2005 17:43:49 +0200
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>Sorry but it doesn't work:
>
>> get(paste("hsa", get("Biosynthesis of steriods", KEGGPATHNAME2ID),
>sep= ""),KEGGPATHID2EXTID)
>Error in get(x, envir, mode, inherits) : variable "Biosynthesis of
>steriods" not find
>
>-----Messaggio originale-----
>Da: bioconductor-bounces at stat.math.ethz.ch
>[mailto:bioconductor-bounces at stat.math.ethz.ch] Per conto di John Zhang
>Inviato: giovedì 16 giugno 2005 16.55
>A: michael.auer at meduniwien.ac.at; rhaddad at genetics.wayne.edu
>Cc: bioconductor at stat.math.ethz.ch
>Oggetto: Re: [BioC] Pathway Information
>
>Suppose you are looking for gene that are involved in human
>"Biosynthesis of 
>steriods" pathway, the following will give you a vector of Entrez Gene
>ids:
>
>>library(KEGG)
>>get(paste("hsa", get("Biosynthesis of steriods", KEGGPATHNAME2ID), sep
>= ""), 
>KEGGPATHID2EXTID)
>
>
>>X-Original-To: jzhang at jimmy.harvard.edu
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>>From: Ramsi Haddad <rhaddad at genetics.wayne.edu>
>>To: michael.auer at meduniwien.ac.at
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>>
>>Dear Michael,
>>	There is a pretty good description in the globaltest vignette.
>Most of
>>the stuff shown below is based on it:
>>
>>library(mgu74av2)
>>library(KEGG)
>>
>>### this next line generates a list of kegg pathways and all
>>### the probe sets that belong in a given pathway.
>>mouse.kegg.sets <- as.list(mgu74av2PATH2PROBE)
>>
>>### the next 3 lines give the names of the pathways from their
>>### kegg ID numbers
>>all.kegg.ids <- ls(KEGGPATHID2NAME)
>>all.kegg.names <- mget(all.kegg.ids, KEGGPATHID2NAME)
>>table.of.keggs <- as.matrix(unlist(all.kegg.names))
>>write.table(table.of.keggs, "keggs.csv", sep=",",col.names=NA,
>>row.names=T)
>>
>>### here's how to get the name of a given kegg pathway:
>>what.is.00010 <- get("00010", KEGGPATHID2NAME) ## this is glycolysis.
>>
>>### here's how to get the probesets in the Glycolysis Path from the
>>mouse array:
>>glycolysis.affyIDs <- get("00010", mgu74av2PATH2PROBE) ## there are 68
>>such probe sets.
>>another.glycolysis.affyIDs <- mouse.kegg.sets[["00010"]] ## more than
>>one way to skin a cat
>>
>>### here's how to get the kegg pathway numbers for anything with
>>"Cholera"
>>colera.kegg.paths.index <- grep("Cholera", table.of.keggs) ## this
>>provides the index
>>colera.keggs <- table.of.keggs[colera.kegg.paths]
>>### here it is in one step:
>>### table.of.keggs[grep("Cholera", table.of.keggs)]
>>
>>hope that gets you started.
>>
>>Ramsi
>>
>>
>>
>>
>>> Hi
>>> 
>>> Can anybody tell me the following
>>> 
>>> I want to identify genes which are located on a certain pathway NF
>Kappa.
>>> How can I obtain such an information. Which package is appropriate
>and
>>> which commands are needed. If any body ever encounterd the same
>problem
>>> please let me know.
>>> 
>>> Michael
>>-- 
>>Ramsi Haddad, Ph.D.
>>Center for Molecular Medicine and Genetics.
>>Functional Genomics Laboratory,
>>Perinatology Research Branch, NICHD, NIH.
>>259 Mack Avenue,
>>Room 3146 Applebaum Bldg.
>>Detroit, MI 48201, USA.
>>
>>phone:(313) 577-2569 / fax:(313) 577-7736
>>
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>Jianhua Zhang
>Department of Medical Oncology
>Dana-Farber Cancer Institute
>44 Binney Street
>Boston, MA 02115-6084
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>

Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084