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 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 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 >> > >>> 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 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 >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>> >>> >>> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane. >> science.biology.informatics.conductor >> >> > [[alternative HTML version deleted]]