non-native GO annotation cannot be successfully introduced into Goseq
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citronxu • 0
@citronxu-24331
Last seen 9 months ago

Hello,

I'm working recently on GO analysis regarding A.thaliana whose database is not included in GOseq package. Then I downloaded the GO annotation from both gene ontology website and TAIR as DAF file (version 2.0/2.1) and was gonna introduce it into R with function readDAF of mgsa. However, during the reading of both files, error has been returned as follow...

Error in readGAF("~/Downloads/gene_association.tair") : 
  At least one DB object ID has multiple DB object symbols or names in gene ontology annotation file.
In addition: Warning messages:
1: In result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
2: In result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().

The error lies on that same object has multiple names, is there any argument can bypass this? or I didn't get the right file...many thanks in advance!!

goseq rnaseq r • 218 views
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@james-w-macdonald-5106
Last seen 8 hours ago
United States

It's not completely clear from your post what you are after. But if I assume you want data for the gene2cat argument for goseq, then you can use the org.At.tair.db package.

> library(org.At.tair.db)

> z <- select(org.At.tair.db, keys(org.At.tair.db), "GOALL")
'select()' returned 1:many mapping between keys and columns
> head(z)
       TAIR      GOALL EVIDENCEALL ONTOLOGYALL
1 AT1G01010 GO:0003674         ISS          MF
2 AT1G01010 GO:0003700         ISS          MF
3 AT1G01010 GO:0005575         ISM          CC
4 AT1G01010 GO:0005622         ISM          CC
5 AT1G01010 GO:0005634         ISM          CC
6 AT1G01010 GO:0006139         IEA          BP

In general you would then do something like

gene2cat.bp <- subset(z, ONTOLOGYALL == "BP")[,1:2]

And similarly for MF and CC if you care to test those ontologies.

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