A GRangesList is a Vector, so that method should work. It just neglected to
resolve the type argument with match.arg() before forwarding. That's now
fixed.

Michael


On Sat, Jun 14, 2014 at 6:27 PM, Valerie Obenchain <vobencha@fhcrc.org>
wrote:

> Hi Janet, Michael,
>
> Janet, were you able to get what you needed by specifying 'type'?
>
> Michael, which method are you referring to when you say it exists but is
> broken? The only method I see that allows a missing 'subject' is
> query="Vector". Maybe we need to add query="GRangesList" subject="missing"?
>
>
> Val
>
>
>
> On 06/11/2014 11:15 AM, Michael Lawrence wrote:
>
>> Turns out I added something else. In this case, the method does exist, but
>> it's just broken. You might have better luck if you specify the type
>> argument to findOverlaps, like type="any".
>>
>>
>> On Wed, Jun 11, 2014 at 10:52 AM, Janet Young <jayoung@fhcrc.org> wrote:
>>
>>  I'm glad that's on your radar already - nice.  I updated all devel
>>> packages this morning - it's not there yet.  Here's my new sessionInfo():
>>>
>>>  sessionInfo()
>>>>
>>> R version 3.1.0 Patched (2014-05-26 r65771)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> locale:
>>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>>> [8] base
>>>
>>> other attached packages:
>>> [1] rtracklayer_1.25.11   GenomicRanges_1.17.18 GenomeInfoDb_1.1.7
>>> [4] IRanges_1.99.15       S4Vectors_0.0.8       BiocGenerics_0.11.2
>>>
>>> loaded via a namespace (and not attached):
>>>   [1] BatchJobs_1.2            BBmisc_1.6
>>> BiocParallel_0.7.2
>>>
>>>   [4] Biostrings_2.33.10       bitops_1.0-6             brew_1.0-6
>>>
>>>   [7] codetools_0.2-8          DBI_0.2-7                digest_0.6.4
>>>
>>> [10] fail_1.2                 foreach_1.4.2
>>> GenomicAlignments_1.1.14
>>> [13] iterators_1.0.7          plyr_1.8.1               Rcpp_0.11.2
>>>
>>> [16] RCurl_1.95-4.1           Rsamtools_1.17.25        RSQLite_0.11.4
>>>
>>> [19] sendmailR_1.1-2          stats4_3.1.0             stringr_0.6.2
>>>
>>> [22] tools_3.1.0              XML_3.98-1.1             XVector_0.5.6
>>>
>>> [25] zlibbioc_1.11.1
>>>
>>> On Jun 10, 2014, at 3:31 PM, Michael Lawrence <lawrence.michael@gene.com
>>> >
>>> wrote:
>>>
>>> I think I might have already added this a couple days ago to devel...
>>> tough to keep it all straight in my head
>>>
>>>
>>> On Tue, Jun 10, 2014 at 3:14 PM, Janet Young <jayoung@fhcrc.org> wrote:
>>>
>>>  Hi again,
>>>>
>>>> This is somewhat related to another request I sent earlier this
>>>> afternoon. Is it possible to implement query-self comparisons (i.e.
>>>> where I
>>>> specify query but not subject) for GRangesList objects?   The
>>>> motivation is
>>>> that I'd like to use the ignoreSelf and ignoreRedundant options in a
>>>> GRangesList comparison.
>>>>
>>>> I mentioned in my other request that I'm looking through a set of genes
>>>> to find pairs that overlap on opposite strands.  I'm now using
>>>> findOverlaps
>>>> on a GRangesList object instead of a GRanges object - that's because I
>>>> want
>>>> to only look at cases where parts of the final spliced transcript
>>>> overlap,
>>>> not cases where a large intron-containing gene has another smaller gene
>>>> nested in an intron.  When I used findOverlaps on the entire genes at
>>>> once
>>>> as GRanges objects, my results included pairs of that nested type, but
>>>> if I
>>>> use the blocks function to get just the exons as a GRangesList object,
>>>> that
>>>> lets me successfully ignore the nested gene case, which is great.
>>>>  However,
>>>> with GRangesList I can't use the query-self comparison and therefore
>>>> can't
>>>> access those useful ignoreSelf and ignoreRedundant options.  I know I
>>>> can
>>>> workaround that too with some effort, but it'd be great to have it as
>>>> part
>>>> of the underlying code.
>>>>
>>>> Again, I've included some code below that should show what I'm trying to
>>>> do.
>>>>
>>>> all the best,
>>>>
>>>> Janet
>>>>
>>>>
>>>> library(rtracklayer)
>>>>
>>>> #### get some drosophila genes as a test case:
>>>> mySession <- browserSession()
>>>> genome(mySession) <- "dm3"
>>>> genes <- ucscTableQuery (mySession, track="flyBaseGene",
>>>> table="flyBaseGene")
>>>> genes <- track(genes)
>>>>
>>>> #### reduce to a smaller example that contains a gene pair of the type
>>>> I'm talking about (CG33797-RA is nested inside CG11152-RA)
>>>> genes <- genes[148:152]
>>>>
>>>> #### remove strand info, as a workaround to not being able to specify
>>>> ignore.strand for a query-self findOverlaps call
>>>> strand(genes) <- "*"
>>>>
>>>> #### using findOverlaps on the genes themselves shows me the nested pair
>>>> (query=3, subject=4)
>>>> findOverlaps( genes, ignoreSelf = TRUE, ignoreRedundant = TRUE)
>>>>
>>>> #### so I'll use blocks to extract only the exonic portions of the genes
>>>> as a GRangesList:
>>>> genes_GRL <- blocks(genes)
>>>>
>>>> #### and use findOverlaps on that GRangesList object, first by
>>>> specifying
>>>> it as both query and subject in the comparison - this gives me more or
>>>> less
>>>> what I want (i.e. it does NOT show the nested pair 3-4), except that
>>>> there's a bunch of filtering to do later.
>>>> findOverlaps( genes_GRL, genes_GRL)
>>>>
>>>> #### ideally, to help me filter the hits I'd like to be able to use
>>>> ignoreSelf and ignoreRedundant, but I can only use those if it's a
>>>> query-self comparison (i.e. only works if no subject is specified)
>>>> findOverlaps( genes_GRL, genes_GRL, ignoreSelf=TRUE,
>>>> ignoreRedundant=TRUE)
>>>> # Error in .local(query, subject, maxgap, minoverlap, type, select,
>>>> ...) :
>>>> #   unused arguments (ignoreSelf = TRUE, ignoreRedundant = TRUE)
>>>>
>>>> #### and it looks like findOverlaps is not implemented for the
>>>> query-self
>>>> case for GRangesList objects
>>>> findOverlaps( genes_GRL)
>>>> # Error in match.arg(type) : 'arg' must be of length 1
>>>>
>>>> sessionInfo()
>>>>
>>>> R version 3.1.0 Patched (2014-05-26 r65771)
>>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>>
>>>> locale:
>>>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>>>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>>
>>>> attached base packages:
>>>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>>>> [8] base
>>>>
>>>> other attached packages:
>>>> [1] rtracklayer_1.25.11   GenomicRanges_1.17.17 GenomeInfoDb_1.1.6
>>>> [4] IRanges_1.99.15       S4Vectors_0.0.8       BiocGenerics_0.11.2
>>>>
>>>> loaded via a namespace (and not attached):
>>>>   [1] BatchJobs_1.2            BBmisc_1.6
>>>> BiocParallel_0.7.2
>>>>   [4] Biostrings_2.33.10       bitops_1.0-6             brew_1.0-6
>>>>   [7] codetools_0.2-8          DBI_0.2-7                digest_0.6.4
>>>> [10] fail_1.2                 foreach_1.4.2
>>>>   GenomicAlignments_1.1.13
>>>> [13] iterators_1.0.7          plyr_1.8.1               Rcpp_0.11.2
>>>> [16] RCurl_1.95-4.1           Rsamtools_1.17.23        RSQLite_0.11.4
>>>> [19] sendmailR_1.1-2          stats4_3.1.0             stringr_0.6.2
>>>> [22] tools_3.1.0              XML_3.98-1.1             XVector_0.5.6
>>>> [25] zlibbioc_1.11.1
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor@r-project.org
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>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>>
>>>
>>>
>>>
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>>
>>
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