On Oct 25, 2011, at 10:40 AM, Assa Yeroslaviz wrote: > Hi all, > > @Martin - thanks for the help it works very good. > > @David - sorry for the misunderstanding. I will see to it, that it > won't > happen again. > BTW, unfortunately your function is not working. > It is patialy my error as I gave no regions with overlaps, but even > after > changing them it just doesn't fit. > > Here is the new data with an overlap in the third gene: > > genetable <- rd.txt("name chr start end str > accession Length > > gen1 4 646752 646838 + MI0005806 86 > gen12 2L 243035 243141 - MI0005821 106 > gen3 2L 159838 159928 + MI0005813 90 > gen7 2L 1831685 1831799 - MI0011290 114 > gen4 2L 2737568 2737661 + MI0017696 93") > loctable <- rd.txt("Chr Start End length > > 4 136532 138654 2122 > 3 139870 141970 2100 > 2L 157838 160440 2602 > X 160834 162966 2132 > 4 204040 208536 4496") > > But I still get: >> apply(genetable, 1, function(x) inregion(x, loctable[, c("Start", > "End")]) ) > [1] FALSE FALSE FALSE FALSE FALSE You just want to pass the start and end columns of genetable > # Helper function > inregion <- function(vec, locs) { + any( apply(locs, 1, function(x) vec["start"]>x[1] & vec["end"]<=x[2])) } > # Test the function > inregion(genetable[2, ], loctable[, c("Start", "End")]) [1] FALSE > # [1] FALSE > > apply(genetable[, 3:4], 1, function(x) inregion(x, loctable[, c("Start", "End")]) ) [1] FALSE FALSE TRUE FALSE FALSE ( I really wish that you would stop crossposting. I am only following your bad practice because you posted my code on BioC.) -- David > > for the single queries I get TRUE: > >> inregion(genetable[3, ], loctable[, c("Start", "End")]) > [1] TRUE > > Do you have Idea, as to how I can fix this problem? > > Thanks and again sorry for the trouble. > > Assa > > On Tue, Oct 25, 2011 at 15:48, Martin Morgan <mtmorgan at="" fhcrc.org=""> > wrote: > >> On 10/25/2011 03:42 AM, Assa Yeroslaviz wrote: >> >>> Hi everybody, >>> >>> I would like to know whether it is possible to compare to tables for >>> certain >>> parameters. >>> I have these two tables: >>> gene table >>> name chr start end str accession Length >>> gen1 4 646752 646838 + MI0005806 86 >>> gen12 2L 243035 243141 - MI0005821 106 >>> gen3 2L 159838 159928 + MI0005813 90 >>> gen7 2L 1831685 1831799 - MI0011290 114 >>> gen4 2L 2737568 2737661 + MI0017696 93 >>> ... >>> >>> localization table: >>> Chr Start End length >>> 4 136532 138654 2122 >>> 3 139870 141970 2100 >>> 2L 157838 158440 602 >>> X 160834 162966 2132 >>> 4 204040 208536 4496 >>> ... >>> >>> I would like to check whether a specific gene lie within a certain >>> region. >>> For example I want to see if gene 3 on chromosome 2L lies within the >>> region >>> given in the second table. >>> >> >> Hi Assa -- >> >> In Bioconductor, use the GenomicRanges package. Create two GRanges >> objects >> >> genes = with(genetable, GRanges(chr, IRanges(start, end), str, >> accession=accession, Length=length) >> locations = with(locationtable, GRanges(Chr, IRanges(Start, End))) >> >> then >> >> olaps = findOverlaps(genes, locations) >> >> queryHits(olaps) and subjectHits(olaps) index each gene with all >> locations >> it overlaps. The definition of 'overlap' is flexible, see ? >> findOverlaps. >> >> Martin >> >> >> >>> What I would like to is like >>> 1. check if the gene lies on a specific chromosome >>> 1.a if no - go to the next line >>> 1.b if yes - go to 2 >>> 2. check if the start position of the gene is bigger than the start >>> position >>> of the localization table AND if it smaller than the end position >>> (if it >>> lies between the start and end positions in the localization table) >>> 2.a if no - go to the next gene >>> 2.b if yes - give it to me. >>> >>> I was having difficulties doing it without running into three >>> interleaved >>> conditional loops (if). >>> >>> I would appreciate any help. >>> >>> Thanks >>> >>> Assa >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor="">>> > >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.**conductor<http: news.gmane.org="" gman="" e.science.biology.informatics.conductor="">>> > >>> >> >> >> -- >> Computational Biology >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >> >> Location: M1-B861 >> Telephone: 206 667-2793 >> > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- guide.html > and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT