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Question: bug report for GenomicRanges::findOverlaps
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gravatar for Kasper Daniel Hansen
7.8 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
GenomicRanges::findOverlaps does not support the same set of values for 'select' and 'type' as the method for Ranges. This is pretty easy to fix, and seems to arise because the GenomicRanges version has the usual function( ... type = c(...)) { type = match.arg(type) } construction, but with type = c("any", "start", "end") instead of type = c("any", "start", "end", "within", "equal"). A better long term fix might be to not do the match.arg inside the method, but directly pass the value of type and select into .findOverlaps.circle (which btw. does exactly this: it simply passes the type and select arguments into findOverlaps) I am specifically interested in type = "within" Kasper
ADD COMMENTlink modified 7.8 years ago by Hervé Pagès ♦♦ 13k • written 7.8 years ago by Kasper Daniel Hansen6.4k
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gravatar for Hervé Pagès
7.8 years ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:
Hi Kasper, Thanks for the report. I'll take care of this and will come back here when it's done. H. On 01/13/2011 09:09 AM, Kasper Daniel Hansen wrote: > GenomicRanges::findOverlaps does not support the same set of values > for 'select' and 'type' as the method for Ranges. This is pretty easy > to fix, and seems to arise because the GenomicRanges version has the > usual > function( ... type = c(...)) { > type = match.arg(type) > } > construction, but with type = c("any", "start", "end") instead of type > = c("any", "start", "end", "within", "equal"). A better long term fix > might be to not do the match.arg inside the method, but directly pass > the value of type and select into .findOverlaps.circle (which btw. > does exactly this: it simply passes the type and select arguments into > findOverlaps) > > I am specifically interested in type = "within" > > Kasper > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
ADD COMMENTlink written 7.8 years ago by Hervé Pagès ♦♦ 13k
Hi Kasper, This is fixed in GenomicRanges 1.3.15 (devel). Cheers, H. On 01/13/2011 11:17 PM, Hervé Pagès wrote: > Hi Kasper, > > Thanks for the report. I'll take care of this and will come back > here when it's done. > > H. > > On 01/13/2011 09:09 AM, Kasper Daniel Hansen wrote: >> GenomicRanges::findOverlaps does not support the same set of values >> for 'select' and 'type' as the method for Ranges. This is pretty easy >> to fix, and seems to arise because the GenomicRanges version has the >> usual >> function( ... type = c(...)) { >> type = match.arg(type) >> } >> construction, but with type = c("any", "start", "end") instead of type >> = c("any", "start", "end", "within", "equal"). A better long term fix >> might be to not do the match.arg inside the method, but directly pass >> the value of type and select into .findOverlaps.circle (which btw. >> does exactly this: it simply passes the type and select arguments into >> findOverlaps) >> >> I am specifically interested in type = "within" >> >> Kasper >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
ADD REPLYlink written 7.7 years ago by Hervé Pagès ♦♦ 13k
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