[BioC] R: Pathway Information

[John Zhang]

Sorry for the typo. steriods should be steroids.

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

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