help documentation for keytypes in annotationdbi packages
2
0
Entering edit mode
kstachelek • 0
@kstachelek-24424
Last seen 4.4 years ago

when using keytypes with annotationdbi I am presented with a vector of keytypes available in a given annotation package. I would like to get more documentation for unfamiliar keytypes. I can easily infer what SYMBOL refers to: RB1, THRB, etc. but others are less familiar. Is this information documented in help pages or anywhere else?

annotation • 1.3k views
ADD COMMENT
1
Entering edit mode
Eric ▴ 10
@2e30d986
Last seen 1 hour ago
United States

Hello, this post is quite old, but I was running into the same issue as I was unclear on what each keytype looks like. Thank you @kayla.interdonato for supplying the previous answer as it is very useful in understanding textually what each keytype represents. My problem was that I still did not know what each keytype visually looked like. I figured out a way to see them.

First, you will want to run keytypes(your Org.db) which will provide you with a list of available keytypes from your particular database. Then you can copy one of the available keytypes and run the following code head(keys(your Org.db, keytpe=the keytype you are interested in)) and you will get back a short list of that particular keytype.

#example
keytypes(org.Hs.eg.db)
head(keys(org.Hs.eg.db, keytypes="REFSEQ"))

I retrieved this answer from the AnnotationDb-objects function website here -> https://www.rdocumentation.org/packages/AnnotationDbi/versions/1.34.4/topics/AnnotationDb-objects under the Examples ## get keys based on unigene comment.

ADD COMMENT
0
Entering edit mode
@kaylainterdonato-17327
Last seen 12 months ago
United States

Trying ?AnnotationDbi::ACCNUM should get you a list of available values for 'columns' and 'keytypes' with their given descriptions. Hope this helps!

ADD COMMENT

Login before adding your answer.

Traffic: 728 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