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
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
>
>
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
>
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
