[Bioc-devel] PANTHER.db GOSLIM_ID hosed?

Hi all, I'm running the latest Bioc + PANTHER.db I think we've got the GOSLIM_TERM where the GOSLIM_ID should be: In the vignette, we have this: R> go_ids <- head(keys(PANTHER.db,keytype="GOSLIM_ID")) R> go_ids ## [1] "GO:003" "GO:165" "GO:166" "GO:228" "GO:375"

Re: [Bioc-devel] PANTHER.db GOSLIM_ID hosed?

>From the head of > PANTHER.db:::.keys function (x, keytype) { t2t <- .type2table(x) t2c <- .type2col(x) I wonder if many of the columns / keytypes are mislabeled, e.g., > PANTHER.db:::.type2col(PANTHER.db) CLASS_IDCLASS_TERM COMPONENT_IDCOMPONENT_TERM

Re: [Bioc-devel] PANTHER.db GOSLIM_ID hosed?

Dear Steve, thanks a lot for pointing out the error! The problem Martin described is exactly the problem addressed in PANTHER.db version 1.02. However the version available on bioconductor is not v1.02. The method type2col in PANTHER.db 1.02 should look like this: > type2col <- function(x){ >

Re: [Bioc-devel] Coverage test badge not updating

The coverage tests were inadvertently not running, but they are now re-enabled. Please let us know if you notice any other problems Jim On Tue, Nov 17, 2015 at 12:16 PM, Leonardo Collado Torres wrote: > Hi, > > In my packages I enabled testing (via testthat) a few weeks ago.

Re: [Bioc-devel] Behavior of select function in AnnotationDbi

I think the answer to 1 should be yes, duplicate keys are allowed. For instance, a vector of ids and a factor that groups the ids somehow (e.g., by experiment), with ids unique in each group. So I'm for step #2. Martin From: Bioc-devel

Re: [Bioc-devel] Behavior of select function in AnnotationDbi

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', ...)

[Bioc-devel] Behavior of select function in AnnotationDbi

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

Re: [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