There is an inconsistency in how select() works in AnnotationDbi when a
user passes in duplicated keys to be mapped, depending on if the mapping is
1:1 or 1:many. It's easiest to show using an example.
> select(org.Hs.eg.db, rep("1", 3), "SYMBOL")
'select()' returned many:1 mapping between keys an
-boun...@r-project.org] on behalf of James W.
MacDonald [jmac...@uw.edu]
Sent: Friday, November 20, 2015 5:30 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Behavior of select function in AnnotationDbi
There is an inconsistency in how select() works in AnnotationDbi when a
user pass
Hi Jim,
I think we should choose the biomaRt model, that is, duplicated are
allowed but silently ignored.
Note that this is also the SQL model. When you do
SELECT * FROM ... WHERE key IN c('key1', 'key2', ...)
duplicated keys don't generate duplicates in the output.
Also note that, like SEL
On 11/20/2015 03:21 PM, Hervé Pagès wrote:
Hi Jim,
I think we should choose the biomaRt model, that is, duplicated are
allowed but silently ignored.
Note that this is also the SQL model. When you do
SELECT * FROM ... WHERE key IN c('key1', 'key2', ...)
^
Hi Hervé,
I think you make a valid point, but I am not sure it conforms to either the
historical expectations for the annotation packages, nor the expected use
case. In other words, the annotation packages have, since the beginning,
returned something that was as close to parallel to the input as
Hi Jim,
I understand the convenience of having an output that is parallel to
the input, especially in the context of the primary use case which is
mapping/cbinding ids to a rectangular object. However for that use
case, "as close to parallel as possible" is not good enough. IMO the
user needs a t
Hi Hervé,
Hmmm. Persuasive arguments. I like it!
I'm pretty close to thinking you are right about this. However there is one
small stumbling block. While select() allows for the look up of multiple
columns simultaneously, mapIds() does not. But I do like your idea of
having a function that guaran
ect.org] on behalf of James W.
MacDonald [jmac...@uw.edu]
Sent: Monday, November 23, 2015 11:16 AM
To: Hervé Pagès
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Behavior of select function in AnnotationDbi
Hi Hervé,
Hmmm. Persuasive arguments. I like it!
I'm pretty close to thinki
;, multiVals="first")
> 'select()' returned 1:many mapping between keys and columns
> BRCA1
> "GO:151"
>
> Martin
>
>
> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of James W
