search for: rangeddata

Hi: I have a two large files (over 300K lines). file 1: Name X UK 199 UK 230 UK 139 ...... UAE 194 UAE 94 File 2: Name X Y UK 140 180 UK 195 240 UK 304 340 .... I want to select X of File 1 and search if it falls in range of X and Y of File 2 and Print only those lines of File 1 that are in range of File 2 X and Y How can it be done it

Dear All, I am trying to finding overlapping regions in two diff datasets for that I am using IRanges. But I am getting an error in the process of doing the overlap. Advance thanks df3.rl<-RangedData(IRanges(start=df3$V3,width=1), + space=df3$start) Error in .normargSEW0(start, "start") : 'start' must be a numeric vector (or NULL) Kumar [[alternative HTML version deleted]]

Dear all, I have some very big data files that look something like this: id chr pos ihh1 ihh2 xpehh rs5748748 22 15795572 0.0230222 0.0268394 -0.153413 rs5748755 22 15806401 0.0186084 0.0268672 -0.367296 rs2385785 22 15807037 0.0198204 0.0186616 0.0602451 rs1981707 22 15809384 0.0299685 0.0176768 0.527892 rs1981708 22 15809434 0.0305465 0.0187227 0.489512 rs11914222 22 15810040 0.0307183

...nt to evaluate the window separately for each > value of chr. > The IRanges package from the Bioconductor project attempts to solve problems like these. For example, to count the number of overlapping intervals at a given position in the chromosome, you would use the coverage() function. The RangedData class is designed to store data like yours and rdapply() makes it easy to perform operations one chromosome at a time. That said, I don't think it has any easy way to solve your problem of calculating quantiles. That's a feature that needs to be added to the package. I could imagine someth...