GEOquery using keywords in R
1
0
Entering edit mode
Didi ▴ 10
@didi-10905
Last seen 7 months ago

Hi,

How to do a GEO query using keywords in R?

I found a few publications but they use the GSE accession number:

GEO_DATASETS <- c("GSE73835")

eset <- getGEOdataObjects(GEO_DATASETS[1])

eset

 

Thanks a lot.

D.

GEO geoquery geometadb • 507 views
ADD COMMENT
0
Entering edit mode

What exactly are you asking? You say something about keywords, but then you try to use a GSE ID, using a non-existent function.
 

ADD REPLY
0
Entering edit mode
I don't know if it's possible instead of using GSE accession numbers to use keywords like c("arabidopsis", "drought") and get all the related GSE accesion numbers. Is there any way to do that?
ADD REPLY
0
Entering edit mode

You could either use the Bioconductor GEOmetadb package, a web interface query on the NCBI website, or eUtils. There are other third-party options as well as similar functionality at EBI.

ADD REPLY
0
Entering edit mode
@sean-davis-490
Last seen 7 days ago
United States

Just guessing that this is what you want:

library(GEOquery)
eset = getGEO('GSE73835')[[1]]
eset
ADD COMMENT

Login before adding your answer.

Traffic: 340 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6