Closed OwenVennard closed 4 years ago
Could you point me to a URL to the CHO-K1 data.
I will have a look in the underlying code to see if I can update the list of biomaRt available databases. If this fails, you can always construct the auxiliary data by hand. It's simply and MSnSet with a binary assay data, with proteins as features (rows) and GO terms as samples (columns). For instance, if you have a csv file with the GO/proteins associations that you pulled from the database, you could create the MSnSet with readMSnSet2
, as illustrated last week at the course.
Do ping me again here if you haven't heard from my by mid next-week.
@lgatto Thanks for getting back in touch and the advice regarding constructing the data manually.
Here is the URL to the CHO-K1 entry, hopefully this is the right thing:
https://www.ensembl.org/Cricetulus_griseus_chok1gshd/Info/Index
Hi all,
I'm interested in utilising the transfer learning capabilities in pRoloc to perform some GO analysis etc (i.e. setAnnotationParams) for Chinese hamster (CHO-K1) cells. From what I understand, the biomaRt package queries the relevant database and retrieves this database. However this species is not currently viewable. I wondered if this could please be added to the list?
Below are species entries from biomart.
Organism: Chinese hamster CHOK1GS (Cricetulus griseus) (Cell line) Genome assembly: CHOK1GS_HDv1 GCA_900186095.1
There is also a separate Chinese hamster database (rather than the cell line).
Organism: Chinese hamster CriGri (CriGri_1.0) Genome assembly: CriGri_1.0 (GCA_000223135.1)
Apologies if in my naivety I'm missing something very obvious as to why this is not currently possible!
Thanks