hi, thanks of the compliments to the package, i'm happy to hear you
liked it! i must acknowledge that part of the design of the package is
the result of conversations i had with Martin, Marc and specially
Valerie during the review process.
i only got to know about VRanges once the package was nearly finished in
its current form and it is in my mind to try to adapt it to that data
structure for the reasons you comment. i haven't explored
'ReportingTools' but i'll give a look at it.
i'll be also very glad if you use it for teaching at Brixen but
beware that this is the first version that entered the release, so it
may have bugs that haven't been discovered yet (a list of known
shortcomings is at the end of the vignette). do not hesitate to report
any problem or feature request that may help using it during the course
and i'll try to fix or add it asap. i'm coming to BioC in Boston, we can
discuss there further directions for a better integration of
VariantFiltering with the rest of the BioC infrastructure.
cheers,
robert.
On 06/18/2014 03:43 PM, Michael Lawrence wrote:
Wow, VariantFiltering is awesome. It's impressive how it integrates all
of the annotation resources so seamlessly. And the shiny app looks very
useful. This should be a model package for where we want to bring
Bioconductor.
You should look into using VRanges instead of GRanges for the return
value of filteredVariants(). It can record the provenance of the filters
if you are using the FilterRules framework. And ReportingTools may be
useful for generating semi-interactive HTML reports.
I'm going to use this in the course next week at Brixen. My tutorial is
already based on the CEU trio, so the vignette integrates perfectly.
Nice work,
Michael
On Wed, Jun 18, 2014 at 6:20 AM, Robert Castelo <robert.cast...@upf.edu
<mailto:robert.cast...@upf.edu>> wrote:
hi Michael,
this souns like if you had a list of variants where you have
annotated their Entrez Gene IDs, which sometimes are NA because
those variance do not overlap any gene and sometimes are repeated
Entrez Gene IDs when two or more of those variants overlap the same
gene :)
at least is the situation i had when programming the
VariantFiltering package, i also could not find a one-liner solution
but you might want to look to what i ended up doing there, in case
it might be also useful for you.
you'll find it in the method "annotateVariants" that dispatches
"OrgDb" objects (i.e., gene-centric annotation packages), within
VariantFiltering/R/__annotationEngine.R
if you take a look at it, do not hesitate to comment if you have any
suggestion to improve this. i also look forward to the
annotation-gurus feedback on this question :)
cheers,
robert.
On 06/18/2014 03:03 PM, Michael Lawrence wrote:
Let's say I have a vector of gene IDs where some are NA, and are
some are
repeated, and I want to map them to gene symbols, where I get
NAs for the
NA IDs or IDs without a symbol. What is the best way to do this?
I tried select() but it gave me a table with unique entries; not
very
convenient. It also does not handle NAs. And totally breaks with
duplicates
using the GENEID key type (kind of works with ENTREZID):
select(Homo.sapiens, GENEID, "SYMBOL", "GENEID")
Error in `[[<-`(`*tmp*`, name, value = list(GENEID = c("245938",
"245939",
:
269 elements in value to replace 1312 elements
Also tried the venerable mget(GENEID, org.Hs.egSYMBOL,
ifnotfound=NA), but
this returns a list and fails with NAs.
What would be nice is something like:
map(Homo.sapiens, GENEID, "SYMBOL", "GENEID", OneToOneOrNone)
where OneToOneOrNone is an assertion that I expect the mappings
to be
one-to-one, so it will unlist() or whatever and throw an error
if the
assertion fails. It should return NA for anything not found, and
for any NA
GENEID. Does something like this already exist?
Michael
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Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514 <tel:%2B34.933.160.514>
fax: +34.933.160.550 <tel:%2B34.933.160.550>
--
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550
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