ann_objs$MAPCOUNTS <- AnnotationDbi:::createMAPCOUNTS(dbconn, prefix) does not work well
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knishida ▴ 20
@knishida-8230
Last seen 14 months ago
United States

Hi 

I'm trying to create tomato orgdb at https://github.com/kozo2/org.Slycopersicum.eg.db

It seems almost OK but the MAPCOUNTS is nil.

Can I ask your comments or suggestions?

 

> install.packages("devtools")
> devtools::install_github("kozo2/org.Slycopersicum.eg.db")
> library("org.Slycopersicum.eg.db")
> org.Slycopersicum.egMAPCOUNTS
integer(0)
annotation orgdb • 1.0k views
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Guido Hooiveld ★ 2.9k
@guido-hooiveld-2020
Last seen 34 minutes ago
Wageningen University, Wageningen, the …

I don't know the answer to your question, but please be informed that on the AnnotationHub such OrgDb for tomato is available. Maybe useful to know. I don't work with tomato, so I don't know how extensive the annotation information really is (AFAIK these are only based on the info available at the NCBI), and whether it is comparable to you OrgDb.

 

> library(AnnotationHub)
> hub = AnnotationHub()
snapshotDate(): 2016-01-25
> query(hub, c("Solanum"))
AnnotationHub with 4 records
# snapshotDate(): 2016-01-25
# $dataprovider: Inparanoid8, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Solanum lycopersicum, Solanum tuberosum
# $rdataclass: Inparanoid8Db, OrgDb
# additional mcols(): taxonomyid, genome, description, tags, sourceurl,
#   sourcetype
# retrieve records with, e.g., 'object[["AH10593"]]'

            title                               
  AH10593 | hom.Solanum_lycopersicum.inp8.sqlite
  AH10606 | hom.Solanum_tuberosum.inp8.sqlite   
  AH48047 | org.Solanum_lycopersicum.eg.sqlite  
  AH48064 | org.Solanum_tuberosum.eg.sqlite     
>
> org.Sl.eg.db <- hub[["AH48047"]]
>
> columns(org.Sl.eg.db)    #which annotation data can be retrieved?
> keytypes(org.Sl.eg.db)    #which identifiers can be queried with?

 

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knishida ▴ 20
@knishida-8230
Last seen 14 months ago
United States

Thanks Guido

I know the tomato OrgDb in AnnotationHub, but the OrgDb does not have some bimaps I need.

(So I'm trying to create new one.)

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What information (bimaps?) is missing from the OrgDb in AnnotationHub? How are you creating the OrgDb package (using code from AnnotationForge)? Providing a code example of the information you're trying to extract and how you are creating the new package will make it easier for others to help.

Also, are you aware of the select() interface for interacting with the OrgDbs? If not, See ?AnnotationDbi::select.

Valerie

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The missing info is like this.

  • LycoCyc pathway annotation
  • The International Tomato Annotation Group (ITAG) ID
  • Sol Genomics Network ID
  • Uniprot ID

I created the sqlite file with https://github.com/kozo2/org.Slycopersicum.eg.db-gen

, and create the OrgDb with https://github.com/kozo2/org.Slycopersicum.eg.db

I'm using AnnotationForge in https://github.com/kozo2/org.Slycopersicum.eg.db-gen/blob/master/tomatoMakeOrgPkg.R

This is just for the sqlite not for the package itself.

A code example is what I already mentioned.

 

 
> install.packages("devtools")
> devtools::install_github("kozo2/org.Slycopersicum.eg.db")
> library("org.Slycopersicum.eg.db")
> org.Slycopersicum.egMAPCOUNTS
integer(0)

 

I just want to check the MAPCOUNTS and know why this line does not work.

https://github.com/kozo2/org.Slycopersicum.eg.db/blob/master/R/objects.R#L119

 

Thank you for your kindness about select() interface.

It seems there is no AnnotationDb object in my package. (but there are AnnDbBimaps)

> require(org.Slycopersicum.eg.db)
> columns(org.Slycopersicum.eg.db)
Error in columns(org.Slycopersicum.eg.db) :
  error in evaluating the argument 'x' in selecting a method for function 'columns': Error: object 'org.Slycopersicum.eg.db' not found

> x <- org.Slycopersicum.egITAG
> mapped_genes <- mappedkeys(x)
> mapped_genes

mapped_genes output is too long so I ommited.

 
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The missing info is like this.

  • LycoCyc pathway annotation
  • The International Tomato Annotation Group (ITAG) ID
  • Sol Genomics Network ID
  • Uniprot ID

I created the sqlite file with https://github.com/kozo2/org.Slycopersicum.eg.db-gen

, and create the OrgDb with https://github.com/kozo2/org.Slycopersicum.eg.db

I'm using AnnotationForge in https://github.com/kozo2/org.Slycopersicum.eg.db-gen/blob/master/tomatoMakeOrgPkg.R

This is just for the sqlite not for the package itself.

A code example is what I already mentioned.

 

 
> install.packages("devtools")
> devtools::install_github("kozo2/org.Slycopersicum.eg.db")
> library("org.Slycopersicum.eg.db")
> org.Slycopersicum.egMAPCOUNTS
integer(0)

 

I just want to check the MAPCOUNTS and know why this line does not work.

https://github.com/kozo2/org.Slycopersicum.eg.db/blob/master/R/objects.R#L119

 

Thank you for your kindness about select() interface.

It seems there is no AnnotationDb object in my package. (but there are AnnDbBimaps)

> require(org.Slycopersicum.eg.db)
> columns(org.Slycopersicum.eg.db)
Error in columns(org.Slycopersicum.eg.db) :
  error in evaluating the argument 'x' in selecting a method for function 'columns': Error: object 'org.Slycopersicum.eg.db' not found

> x <- org.Slycopersicum.egITAG
> mapped_genes <- mappedkeys(x)
> mapped_genes

mapped_genes output is too long so I ommited.

 
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Entering edit mode

The missing info is like this.

  • LycoCyc pathway annotation
  • The International Tomato Annotation Group (ITAG) ID
  • Sol Genomics Network ID
  • Uniprot ID

I created the sqlite file with https://github.com/kozo2/org.Slycopersicum.eg.db-gen

, and create the OrgDb with https://github.com/kozo2/org.Slycopersicum.eg.db

I'm using AnnotationForge in https://github.com/kozo2/org.Slycopersicum.eg.db-gen/blob/master/tomatoMakeOrgPkg.R

This is just for the sqlite not for the package itself.

A code example is what I already mentioned.

> install.packages("devtools")
> devtools::install_github("kozo2/org.Slycopersicum.eg.db")
> library("org.Slycopersicum.eg.db")
> org.Slycopersicum.egMAPCOUNTS
integer(0)

 

I just want to check the MAPCOUNTS and know why this line does not work.

https://github.com/kozo2/org.Slycopersicum.eg.db/blob/master/R/objects.R#L119

 

Thank you for your kindness about select() interface.

It seems there is no AnnotationDb object in my package. (but there are AnnDbBimaps)

> require(org.Slycopersicum.eg.db)
> columns(org.Slycopersicum.eg.db)
Error in columns(org.Slycopersicum.eg.db) :
  error in evaluating the argument 'x' in selecting a method for function 'columns': Error: object 'org.Slycopersicum.eg.db' not found
> x <- org.Slycopersicum.egITAG
> mapped_genes <- mappedkeys(x)
> mapped_genes

mapped_genes output is too long so I ommited.

 
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knishida ▴ 20
@knishida-8230
Last seen 14 months ago
United States

I'm sorry I don't know why my posts were done redundantly.

Could you please delete the duplicate posts?

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knishida ▴ 20
@knishida-8230
Last seen 14 months ago
United States

I slightly update the repository like this https://github.com/kozo2/org.Slycopersicum.eg.db/commit/270527696df082246b05bf5f1544e7541414a909

Now there is an AnnotationDb object in my package. (and I can select the columns)

> library(org.Slycopersicum.eg.db)
> columns(org.Slycopersicum.eg.db)
 [1] "CHR"         "ec"          "enzyme"      "EVIDENCE"    "EVIDENCEALL"
 [6] "GENENAME"    "GID"         "GO"          "GOALL"       "ITAG"       
[11] "lycocyc"     "ONTOLOGY"    "ONTOLOGYALL" "SGN"         "SYMBOL"     
[16] "UNIPROT"    
> org.Slycopersicum.egMAPCOUNTS
integer(0)

But the MAPCOUNTS is still nil...

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I'm fairly new to the annotations so I had to seek counsel from Marc on this one (thanks Marc!).

The fact that your original OrgDb did not have an AnnotationDb object indicates you had an old version of AnnotationForge. Current release is 1.12.2 and devel is 1.13.8. It looks like you updated at some point and the second package did contain an AnnotationDb. When you post a question on the support site please include the output of sessionInfo() so we can see what versions you're using.

The bimaps have been replaced with the select() interface. The makeOrgPackage() was not intended to support bimaps but instead it creates an OrgDb from any set of IDs you choose. (Old OrgDb packages with bimaps were created with hard-coded with templates etc.) The important things to check in an OrgDb made with makeOrgPackage() is that an AnnotationDbi object is present and the select() interface returns the fields originally defined. MAPCOUNTS is not important or relevant here.

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