where is the "getHomolog" function in biomaRt?
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Roger Liu ▴ 260
@roger-liu-2141
Last seen 9.6 years ago
Dear list, After asking how to do cross specices annotation. I tried BiomaRt, and find there is direct function "getHomolog" described in its manual to do this. But when I try to use it, it gave me the error: "Error: could not find function "getHomolog" Could anyone explain this to me? where should I found a version with this fucntion? Thanks. -Roger
Annotation biomaRt Annotation biomaRt • 1.2k views
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 7.7 years ago
United States
You could also use the inparanoid packages which provide mappings based on data generated by the inparanoid algorithm. # Lets suppose you started with the platform hgu95av2.db # And had the following ids: library(hgu95av2.db) ids = c("1000_at","1001_at","1002_f_at","1003_s_at","1004_at" ,"1005_at") # You would 1st want to get the entrez gene IDs (you need some sort of universal gene ID for the next step) EGIDs = mget(ids, hgu95av2ENTREZID, ifnotfound=NA) # Then you could use the idConverter function to convert from human to mouse like this result = idConverter(EGIDs, srcSpecies="HOMSA", destSpecies="MUSMU",srcIDType="EG", destIDType="EG") Does that help? Marc On 03/24/2010 09:27 AM, zrl wrote: > Dear list, > > After asking how to do cross specices annotation. I tried BiomaRt, and > find there is direct function "getHomolog" described in its manual to > do this. > > But when I try to use it, it gave me the error: > > "Error: could not find function "getHomolog" > > Could anyone explain this to me? where should I found a version with > this fucntion? Thanks. > > > -Roger > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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Roger Liu ▴ 260
@roger-liu-2141
Last seen 9.6 years ago
I figured it out, it depends on what version you used. My linux version is fine with this function. On Wed, Mar 24, 2010 at 12:27 PM, zrl <zrl1974 at="" gmail.com=""> wrote: > Dear list, > > After asking how to do cross specices annotation. I tried BiomaRt, and > find there is direct function "getHomolog" described in its manual to > do this. > > But when I try to use it, it gave me the error: > > "Error: could not find function "getHomolog" > > Could anyone explain this to me? where should I found a version with > this fucntion? Thanks. > > > -Roger >
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Dear Zrl, I think this function has been retired a long time ago. For replacement, please have a look at section 4.11 of the package vignette, and the getLDS function. Best wishes Wolfgang > Dear list, > > After asking how to do cross specices annotation. I tried BiomaRt, and > find there is direct function "getHomolog" described in its manual to > do this. > > But when I try to use it, it gave me the error: > > "Error: could not find function "getHomolog" > > Could anyone explain this to me? where should I found a version with > this fucntion? Thanks. > > > -Roger > -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber/contact
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