On 10/16/2010 12:28 PM, joseph wrote: > Hi Michael > my goal is to create promoter regions 350 bases upstream and 150 downstream of > the TSS. > > > I used GRanges and not IRanges, as you suggested: >> refGene = transcripts(makeTranscriptDbFromUCSC("hg18", "refGene")) >> refGene_promoter=resize(flank(hg18_refGene, 350), 500) > Warning message: > In `start<-`(`*tmp*`, value = c(58604L, 313405L, 313405L, 313405L, : > trimmed start values to be positive > Am I doing right and what is the meaning of the Warning message? Joseph -- One of your TSS is close enough to 1 that trying to define the region makes it less than 1. > gr = GRanges("chrA", IRanges(10, width=1), seqlengths=c(chrA=100)) > flank(gr, 11) GRanges with 1 range and 0 elementMetadata values seqnames ranges strand | <rle> <iranges> <rle> | [1] chrA [1, 9] * | seqlengths chrA 100 Warning message: In `start<-`(`*tmp*`, value = -1L) : trimmed start values to be positive This check is done when you've provided GRanges with a seqlength. Nothing to be concerned about, except if it doesn't make (biological) sense for the TSS to be that close to the start of the sequence... Martin > Thank you for your help > Joseph > > > ________________________________ > From: Michael Lawrence <lawrence.michael at="" gene.com=""> > > Cc: bioconductor at stat.math.ethz.ch > Sent: Fri, October 15, 2010 6:23:06 PM > Subject: Re: [BioC] help with flank() > > > > > > > Hello >> I have an IRanges object ir1: >> ir1 <- IRanges(c(100,500), c(200,600)) >>> ir1 >> IRanges of length 2 >> start end width >> [1] 100 200 101 >> [2] 500 600 101 >> >> can you please show me how to use flank() to create a second IRanges object ir2 >> with coordinates that are 50 upstream of ir1 'start' and 20 downstream of the >> same ir1 'start'? >> >> > > This really isn't possible with flank() all by itself unfortunately. With both = > TRUE, it will define a range that overlaps the start, but it's symmetric, not > 50/20. > > You can define ranges for the 50bp upstream of start: > > upstream <- flank(x, 50) > > And then resize to 70, anchoring on the start, so that they extend 20 into the > gene: > > resize(upstream, 70) > > Note that you'll want to use GRanges, not IRanges, to do this based on the > strand (and thus the direction of transcription). > > If you're just going to use IRanges, just do: > > IRanges(start(x) - 50, width = 70) > > > ir2 should look like this: >> start end width >> [1] 50 120 71 >> [2] 450 520 71 >> >> Thanks >> joseph >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> 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 at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: 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