[BioC] hs.Mm.inp.db problem

Iain Gallagher iaingallagher at btopenworld.com
Thu Nov 12 22:28:27 CET 2009


Thanks Mark

Works a treat.

Iain

--- On Thu, 12/11/09, Marc Carlson <mcarlson at fhcrc.org> wrote:

> From: Marc Carlson <mcarlson at fhcrc.org>
> Subject: Re: [BioC] hs.Mm.inp.db problem
> To: "Iain Gallagher" <iaingallagher at btopenworld.com>
> Cc: bioconductor at stat.math.ethz.ch
> Date: Thursday, 12 November, 2009, 20:29
> Hi Iain,
> 
> The trouble you are having is because inparanoid uses
> Jackson lab IDs
> (MGI) instead of ensembl protein IDs when representing
> mouse.
> 
> So this script should work better:
> 
> library(hom.Mm.inp.db)
> library(org.Mm.eg.db)
> library(org.Hs.eg.db)
> 
> dataIn <- c('Ints7', 'Upp1', 'Cdc2a')
> egs <- mget(dataIn,revmap(org.Mm.egSYMBOL))
> 
> ## this is what you want right here:
> mouseProtIds <- mget(unlist(egs),org.Mm.egMGI)  
> mouseProtIds <- mouseProtIds[!is.na(mouseProtIds)]
> 
> rawHumanProtIds <-
> mget(unlist(mouseProtIds),hom.Mm.inpHOMSA,ifnotfound=NA)
> 
> ##etc.
> 
> Hope this helps,
> 
> 
>   Marc
> 
> 
> 
> Iain Gallagher wrote:
> > Hi - Just a follow up post.
> >
> > The title should of course be hom.Mm.inp.db problem
> and session info is below:
> >
> >   
> >> sessionInfo()
> >>     
> > R version 2.9.0 (2009-04-17) 
> > x86_64-pc-linux-gnu 
> >
> > locale:
> >
> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats     graphics 
> grDevices utils     datasets 
> methods   base     
> >
> > other attached packages:
> > [1] org.Hs.eg.db_2.2.11 
> org.Mm.eg.db_2.2.11  hom.Mm.inp.db_2.2.11
> > [4] RSQLite_0.7-1       
> DBI_0.2-4           
> AnnotationDbi_1.6.0 
> > [7] Biobase_2.4.1       
> >   
> > Thanks
> >
> > Iain
> >
> > --- On Thu, 12/11/09, Iain Gallagher <iaingallagher at btopenworld.com>
> wrote:
> >
> >   
> >> From: Iain Gallagher <iaingallagher at btopenworld.com>
> >> Subject: [BioC] hs.Mm.inp.db problem
> >> To: bioconductor at stat.math.ethz.ch
> >> Date: Thursday, 12 November, 2009, 18:41
> >> Hello List
> >>
> >> I am trying to map ~5000 mouse genes to human
> genes using
> >> the inparanoid package and I am failing
> miserably!
> >>
> >> Having followed the example in the documentation I
> can't
> >> get any of my 5000 mouse genes converted to human
> EG ids.
> >>
> >> Example follows with 3 genes only:
> >>
> >> rm(list=ls())
> >>
> >> library(hom.Mm.inp.db)
> >> library(org.Mm.eg.db)
> >> library(org.Hs.eg.db)
> >>
> >> #mouse genes in as symbols
> >> dataIn <- c('Ints7', 'Upp1', 'Cdc2a')
> >>
> >> #map these to mouse EG ids
> >> egIds <- revmap(org.Mm.egSYMBOL)
> >> mapped <- mappedkeys(egIds)
> >> egIds <- as.list(egIds[mapped])
> >> ind <- which(names(egIds)%in%dataIn)
> >> egIdsIn <- egIds[ind]
> >> #map these IDs to ENSEMBL protein Ids as used for
> the
> >> inparanoid mapping
> >> mouseProtIds <-
> >> mget(unlist(egIdsIn),org.Mm.egENSEMBLPROT)
> >> mouseProtIds <-
> mouseProtIds[!is.na(mouseProtIds)]
> >>
> >> #this is the point of failure!
> >> rawHumanProtIds <-
> >>
> mget(unlist(mouseProtIds),hom.Mm.inpHOMSA,ifnotfound=NA)
> >>
> >>
> >> the returned list is full of NA
> >>
> >> Using biomart on the Ensembl site I can get:
> >>
> >> Ensembl Transcript ID    Human Ensembl
> Protein
> >> ID
> >> ENSMUST00000020099   
> >>    ENSP00000397973
> >>
> >> For example, for Cdc2a, so I know there are
> homologs there,
> >> but for some reason the inparanoid package is not
> working
> >> for me.
> >> Using the example in the documentation it does
> work though
> >> so I'm assuming the mistake is with me.
> >>
> >> Can anyone help with this (more curiosity now - I
> can get
> >> the data through biomart)?
> >>
> >> Cheers
> >>
> >> Iain
> >>
> >> _______________________________________________
> >> 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
> >>
> >>     
> >
> > _______________________________________________
> > 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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