Question

Are AH52264, AH66175, and AH70594 duplicates?

0

Entering edit mode

Aditya ▴ 160

@aditya-7667

Last seen 2.5 years ago

Germany

Are AH52264, AH66175 and AH70594 duplicates, arisen due to automated snapshotting of the same resource at different dates?

ah <- AnnotationHub()            # all
ucsc <- query(ah, 'UCSC')        # ucsc 
txdbs <- query(ucsc, 'TxDb')     # txdb 
txdbs
       title                                    
     AH52263 | TxDb.Mmusculus.UCSC.mm10.ensGene.sqlite  
     AH52264 | TxDb.Mmusculus.UCSC.mm10.knownGene.sqlite
     AH52265 | TxDb.Mmusculus.UCSC.mm9.knownGene.sqlite 
     AH66175 | TxDb.Mmusculus.UCSC.mm10.knownGene.sqlite
     AH70594 | TxDb.Mmusculus.UCSC.mm10.knownGene.sqlite

AnnotationHub • 1.4k views

ADD COMMENT • link updated 5.2 years ago by shepherl 4.1k • written 5.2 years ago by Aditya ▴ 160

score 2 · Accepted Answer · 2019-10-18

2

Entering edit mode

shepherl 4.1k

@lshep

Last seen 1 day ago

United States

We rebuild the TxDb per release cycle to account for any changes; A new version but for the same genome build. The most recent will likely be what you want but we don't strictly replace so people could replicate older analysis.

ADD COMMENT • link 5.2 years ago shepherl 4.1k

0

Entering edit mode

Thank you Lori :-) .

ADD REPLY • link 5.2 years ago Aditya ▴ 160

1

Entering edit mode

Also note that this information is available, so you can check for yourself.

> z <- query(hub, c("UCSC","TxDb","mus musculus"))
> z
AnnotationHub with 5 records
# snapshotDate(): 2019-10-17 
# $dataprovider: UCSC
# $species: Mus musculus
# $rdataclass: TxDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH52263"]]' 

            title                                    
  AH52263 | TxDb.Mmusculus.UCSC.mm10.ensGene.sqlite  
  AH52264 | TxDb.Mmusculus.UCSC.mm10.knownGene.sqlite
  AH52265 | TxDb.Mmusculus.UCSC.mm9.knownGene.sqlite 
  AH66175 | TxDb.Mmusculus.UCSC.mm10.knownGene.sqlite
  AH70594 | TxDb.Mmusculus.UCSC.mm10.knownGene.sqlite

> names(mcols(z))
 [1] "title"              "dataprovider"       "species"           
 [4] "taxonomyid"         "genome"             "description"       
 [7] "coordinate_1_based" "maintainer"         "rdatadateadded"    
[10] "preparerclass"      "tags"               "rdataclass"        
[13] "rdatapath"          "sourceurl"          "sourcetype"        

> mcols(z)[,c("title","rdatadateadded")]
DataFrame with 5 rows and 2 columns
                                            title rdatadateadded
                                      <character>    <character>
AH52263   TxDb.Mmusculus.UCSC.mm10.ensGene.sqlite     2016-12-22
AH52264 TxDb.Mmusculus.UCSC.mm10.knownGene.sqlite     2016-12-22
AH52265  TxDb.Mmusculus.UCSC.mm9.knownGene.sqlite     2016-12-22
AH66175 TxDb.Mmusculus.UCSC.mm10.knownGene.sqlite     2018-10-22
AH70594 TxDb.Mmusculus.UCSC.mm10.knownGene.sqlite     2019-05-01

ADD REPLY • link 5.2 years ago James W. MacDonald 67k

0

Entering edit mode

Thankyou James. Knowing it is policy (for backward compatibility) rather than artifact helps to appreciate the redundancy :-)

ADD REPLY • link 5.2 years ago Aditya ▴ 160