Error in .local(x, i, j = j, ...) : 'i' must be length 1 in using OrganismDbi to create org.XX.eg.db
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amafon95 • 0
@amafon95-23956
Last seen 13 months ago

Hallo!

I am currently writing my masters thesis and am trying to create an org.XX.eg.db object for Pon abelii, for a GO analysis with the R-package clusterProfiler, and this requires this kind of object. For orangutan this does not exists as an already available R-package. I created a TxDB object and wanted to use the command "makeOrganismDbFromTxDb(txdb_Orang, keytype="GENEID", orgdb=NA)", but unfortunately I get one error message I can´t solve:

Error in .local(x, i, j = j, ...) : 'i' must be length 1

Also, the help websites on the internet do not show any helping entries, except updating the packages. This error also appears when I try to create the eg.db object with the commands makeOrganismDbFromBiomart and makeOrganismDbFromUCSC from the ‘OrganismDbi’ package.

Do you might have an idea how I can create this object? I would really appreciate an answer.

Kind regards Amanda

annotation • 483 views
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@james-w-macdonald-5106
Last seen 16 hours ago
United States

The function you are using is intended to make an OrganismDb package, which is distinct from an OrgDb package. The former being a meta-package that combines a TxDb, an OrgDb and the GO.db package so you can make queries that span information in those packages, and the latter being a package that contains functional annotations about an organism (as compared to the genomic information in a TxDb package).

Anyway, you don't have to make anything yourself. You can just get what you need from the AnnotationHub:

> library(AnnotationHub)

> hub <- AnnotationHub()
snapshotDate(): 2020-04-27

> query(hub, "Pongo abelii")
AnnotationHub with 166 records
# snapshotDate(): 2020-04-27
# $dataprovider: Ensembl, UCSC, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, Inpar...
# $species: Pongo abelii
# $rdataclass: TwoBitFile, GRanges, EnsDb, OrgDb, Inparanoid8Db
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH6283"]]' 

            title                                  
  AH6283  | Assembly                               
  AH6284  | RefSeq Genes                           
  AH6285  | Ensembl Genes                          
  AH6286  | Genscan Genes                          
  AH6287  | Orangutan mRNAs                        
  ...       ...                                    
  AH80673 | org.Pongo_abelii.eg.sqlite          <-- That is what we want   
  AH82835 | Pongo_abelii.PPYG2.cdna.all.2bit       
  AH82836 | Pongo_abelii.PPYG2.dna_rm.toplevel.2bit
  AH82837 | Pongo_abelii.PPYG2.dna_sm.toplevel.2bit
  AH82838 | Pongo_abelii.PPYG2.ncrna.2bit       

> orgdb <- hub[["AH80673"]]
downloading 1 resources
retrieving 1 resource
  |======================================================================| 100%

loading from cache
> orgdb
OrgDb object:
| DBSCHEMAVERSION: 2.1
| DBSCHEMA: NOSCHEMA_DB
| ORGANISM: Pongo abelii
| SPECIES: Pongo abelii
| CENTRALID: GID
| Taxonomy ID: 9601
| Db type: OrgDb
| Supporting package: AnnotationDbi

Please see: help('select') for usage information

## do something random to show functionality

> select(orgdb, head(keys(orgdb)), "SYMBOL")
'select()' returned 1:1 mapping between keys and columns
     GID SYMBOL
1 808473    ND1
2 808474   ATP8
3 808475   COX2
4 808476    ND6
5 808477   ND4L
6 808478    ND2
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Thank you, that works perfectly! That is an even better solution than I was hoping for.

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Hello,

I wanted to check some information about the annotation file I retrieved from the package. But suddenly when I use the query(hub, "Pongo abelii") command, I get an error message I don´t understand:

hub <- AnnotationHub() snapshotDate(): 2020-04-27

query(hub, "Pongo abelii") Error in autosocket() : banknameSocket not found, try choosebank() first

What happened from one day to the other, that suddenly this command does not work like before?

Kind regards!

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autosocket() is defined in the seqinr package, and my guess is that you have selected seqinr::query(). Be explicit about the function that you are using, AnnotationHub::query(hub, "pongo abelii').

> seqinr::query(hub, "Pongo abelii")
Error in autosocket() : banknameSocket not found, try choosebank() first
> AnnotationHub::query(hub, "Pongo abelii")
AnnotationHub with 166 records
# snapshotDate(): 2020-07-20
# $dataprovider: Ensembl, UCSC, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, Inpar...
# $species: Pongo abelii
...
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