Hi Steve I can see that statement in the findOverlaps method. Do I need to write my own function to do this as 'ignore.strand' is not an allowed argument in standard function. What are the steps to do this? Thanks Fahim On Fri, Jan 6, 2012 at 4:41 PM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > Hi Fahim, > > > On Fri, Jan 6, 2012 at 4:08 PM, Fahim Mohammad <fahim.md@gmail.com> wrote: > > Hi > > findOverlap function depends on the 'strand'edness of the subject and > > query. In the example below, I am using findOverlap function to find > > overlapping ranges. Is there a way to completely ignore this feature and > > report all overlaps. > > [snip] > > Do this in your R workspace: > > R> library(GenomicRanges) > R> getMethod('findOverlaps', c("GenomicRanges", "GenomicRanges")) > > And notice that the findOverlaps method when called on GenomicRanges > objects has an `ignore.strand` argument that you can set to TRUE to > get what you are want, so, do: > > R> o <- findOverlaps(grQuery, grSubject, ignore.strand=TRUE) > > HTH, > -steve > > > grSubject <- > > GRanges( > > seqnames =Rle(rep("chr1", 7)), > > ranges = IRanges(c(1,5,15,22,5,15,22),c(11,8,20,30,8,17,25)), > > strand = Rle(strand(c("-", rep("+",6)))), > > name = c('a', 'b','b','b','c','c','c') > > ) > >> grSubject > > GRanges with 7 ranges and 1 elementMetadata value: > > seqnames ranges strand | name > > <rle> <iranges> <rle> | <character> > > [1] chr1 [ 1, 11] - | a > > [2] chr1 [ 5, 8] + | b > > [3] chr1 [15, 20] + | b > > [4] chr1 [22, 30] + | b > > [5] chr1 [ 5, 8] + | c > > [6] chr1 [15, 17] + | c > > [7] chr1 [22, 25] + | c > > --- > > seqlengths: > > chr1 > > NA > > > > > > grQuery <- > > GRanges( > > seqnames =Rle(rep("chr1", 3)), > > ranges = IRanges(c(6,14,22),c(10,16,27)), > > strand = Rle(strand(rep("-",3))), > > name = c('x', 'y','z') > > ) > >> grQuery > > GRanges with 3 ranges and 1 elementMetadata value: > > seqnames ranges strand | name > > <rle> <iranges> <rle> | <character> > > [1] chr1 [ 6, 10] - | x > > [2] chr1 [14, 16] - | y > > [3] chr1 [22, 27] - | z > > --- > > seqlengths: > > chr1 > > NA > > > > as.matrix(findOverlaps(grQuery, grSubject)) > > query subject > > [1,] 1 1 > > > > > > When I change the strand of the query like this: > > grQuery <- > > GRanges( > > seqnames =Rle(rep("chr1", 3)), > > ranges = IRanges(c(6,14,22),c(10,16,27)), > > strand = Rle(strand(c("-", rep("+",2)))), > > name = c('x', 'y','z') > > ) > > > > I get > >> as.matrix(findOverlaps(grQuery, grSubject)) > > query subject > > [1,] 1 1 > > [2,] 2 3 > > [3,] 2 6 > > [4,] 3 4 > > [5,] 3 7 > >> > > > > > > Thanks > > > > Fahim > > > > [[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 > > > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > [[alternative HTML version deleted]]

Thanks Steve. I resolved the problem. Actually I was using ignore.strand option with RangedData object. Thanks again. Fahim On Fri, Jan 6, 2012 at 4:41 PM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > Hi Fahim, > > > On Fri, Jan 6, 2012 at 4:08 PM, Fahim Mohammad <fahim.md@gmail.com> wrote: > > Hi > > findOverlap function depends on the 'strand'edness of the subject and > > query. In the example below, I am using findOverlap function to find > > overlapping ranges. Is there a way to completely ignore this feature and > > report all overlaps. > > [snip] > > Do this in your R workspace: > > R> library(GenomicRanges) > R> getMethod('findOverlaps', c("GenomicRanges", "GenomicRanges")) > > And notice that the findOverlaps method when called on GenomicRanges > objects has an `ignore.strand` argument that you can set to TRUE to > get what you are want, so, do: > > R> o <- findOverlaps(grQuery, grSubject, ignore.strand=TRUE) > > HTH, > -steve > > > grSubject <- > > GRanges( > > seqnames =Rle(rep("chr1", 7)), > > ranges = IRanges(c(1,5,15,22,5,15,22),c(11,8,20,30,8,17,25)), > > strand = Rle(strand(c("-", rep("+",6)))), > > name = c('a', 'b','b','b','c','c','c') > > ) > >> grSubject > > GRanges with 7 ranges and 1 elementMetadata value: > > seqnames ranges strand | name > > <rle> <iranges> <rle> | <character> > > [1] chr1 [ 1, 11] - | a > > [2] chr1 [ 5, 8] + | b > > [3] chr1 [15, 20] + | b > > [4] chr1 [22, 30] + | b > > [5] chr1 [ 5, 8] + | c > > [6] chr1 [15, 17] + | c > > [7] chr1 [22, 25] + | c > > --- > > seqlengths: > > chr1 > > NA > > > > > > grQuery <- > > GRanges( > > seqnames =Rle(rep("chr1", 3)), > > ranges = IRanges(c(6,14,22),c(10,16,27)), > > strand = Rle(strand(rep("-",3))), > > name = c('x', 'y','z') > > ) > >> grQuery > > GRanges with 3 ranges and 1 elementMetadata value: > > seqnames ranges strand | name > > <rle> <iranges> <rle> | <character> > > [1] chr1 [ 6, 10] - | x > > [2] chr1 [14, 16] - | y > > [3] chr1 [22, 27] - | z > > --- > > seqlengths: > > chr1 > > NA > > > > as.matrix(findOverlaps(grQuery, grSubject)) > > query subject > > [1,] 1 1 > > > > > > When I change the strand of the query like this: > > grQuery <- > > GRanges( > > seqnames =Rle(rep("chr1", 3)), > > ranges = IRanges(c(6,14,22),c(10,16,27)), > > strand = Rle(strand(c("-", rep("+",2)))), > > name = c('x', 'y','z') > > ) > > > > I get > >> as.matrix(findOverlaps(grQuery, grSubject)) > > query subject > > [1,] 1 1 > > [2,] 2 3 > > [3,] 2 6 > > [4,] 3 4 > > [5,] 3 7 > >> > > > > > > Thanks > > > > Fahim > > > > [[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 > > > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > [[alternative HTML version deleted]]