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Htseq-count Vs CountOverlap function in IRanges biofreak General 5 06-29-2011 10:36 AM
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Old 01-26-2012, 01:31 AM   #1
Kumar10
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Location: Hyderbad, India

Join Date: Jan 2012
Posts: 3
Default Need help in IRanges

Hi
I am using IRanges for finding overlaps in genomic ranges. so I would like to know whether there is any function or any method by which i can determine that i will get a result of overlaps which are above the threshold level which i determine. Thank you in advance.
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Old 01-26-2012, 03:00 PM   #2
Dario1984
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Location: Sydney, Australia

Join Date: Jun 2011
Posts: 166
Default

Hello,

You should try using the package GenomicRanges. Click here for its home page. It's much easier to handle chromosomal data with it. It's made by the same people who made IRanges. In this example I show you how to find all regions that have 2 or more reads.

Code:
library(GenomicRanges)
g <- GRanges(c("chr1", "chr1"), IRanges(start = c(5, 10), end = c(15, 20)), strand = '+')
g
GRanges with 2 ranges and 0 elementMetadata values:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1  [ 5, 15]      +
  [2]     chr1  [10, 20]      +
  ---
  seqlengths:
   chr1
     NA
slice(coverage(g), 2)[["chr1"]]
Views on a 20-length Rle subject

views:
    start end width
[1]    10  15     6 [2 2 2 2 2 2]
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