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'thappen again. BTW, unfortunately your function is not working.It is patialy my error as I gave no regions with overlaps, but even afterchanging 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. AssaOn Tue, Oct 25, 2011 at 15:48, Martin Morgan <[email protected]> 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 objectsgenes = 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.MartinWhat 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 positionof the localization table AND if it smaller than the end position (if itlies 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 interleavedconditional loops (if). I would appreciate any help. Thanks Assa [[alternative HTML version deleted]] ______________________________**_________________ Bioconductor mailing list [email protected]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/gmane.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]] ______________________________________________ [email protected] 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 ______________________________________________ [email protected] 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.
