[Bioc-devel] Behavior of select function in AnnotationDbi
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 SELECT, even if the keys supplied to
biomaRt::getBM() (via the 'values' arg) don't contain duplicates
and if all the mappings are 1-to-1, biomaRt::getBM() is not
guarantee to preserve order.
Generally speaking having duplicates in the input produce duplicates
in the output is useful in vectorized operations when the output
is expected to be parallel to the input. Vectorized operations also
need to propagate NAs and to preserve order. However, like SELECT
and biomaRt::getBM(), select() cannot produce an output that is
parallel to the input *in general*.
It seems that the current philosophy for select() is to emit a note
or a warning every time the output is not parallel to the input.
Personally I find this too noisy and not that useful.
Thanks,
H.
On 11/20/2015 02:30 PM, James W. MacDonald wrote:
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 and columns ENTREZID SYMBOL 1 1 A1BG 2 1 A1BG 3 1 A1BG
select(org.Hs.eg.db, rep("1", 3), "GO")
'select()' returned many:many mapping between keys and columns ENTREZID GO EVIDENCE ONTOLOGY 1 1 GO:0003674 ND MF 2 1 GO:0003674 ND MF 3 1 GO:0003674 ND MF This is obviously a bug. A single query for that ID results in this:
select(org.Hs.eg.db, "1", "GO")
'select()' returned 1:many mapping between keys and columns ENTREZID GO EVIDENCE ONTOLOGY 1 1 GO:0003674 ND MF 2 1 GO:0005576 IDA CC 3 1 GO:0005615 IDA CC 4 1 GO:0008150 ND BP 5 1 GO:0070062 IDA CC 6 1 GO:0072562 IDA CC So the returned results are completely borked. However, the question I have is what should be returned? To be consistent with the first example, it should be the output expected for a single key, repeated three times, which I have patched AnnotationDbi to do:
select(org.Hs.eg.db, rep("1", 3), "GO")
'select()' returned many:many mapping between keys and columns
ENTREZID GO EVIDENCE ONTOLOGY
1 1 GO:0003674 ND MF
2 1 GO:0005576 IDA CC
3 1 GO:0005615 IDA CC
4 1 GO:0008150 ND BP
5 1 GO:0070062 IDA CC
6 1 GO:0072562 IDA CC
7 1 GO:0003674 ND MF
8 1 GO:0005576 IDA CC
9 1 GO:0005615 IDA CC
10 1 GO:0008150 ND BP
11 1 GO:0070062 IDA CC
12 1 GO:0072562 IDA CC
13 1 GO:0003674 ND MF
14 1 GO:0005576 IDA CC
15 1 GO:0005615 IDA CC
16 1 GO:0008150 ND BP
17 1 GO:0070062 IDA CC
18 1 GO:0072562 IDA CC
So, two questions.
1. Should duplicate keys be allowed, or should duplicates be removed
before querying the database, preferably with a message saying that dups
were removed?
2. If the answer to #1 is yes, then to be consistent, I will just commit
the patch I have made to both devel and release.
Best,
Jim
Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319