Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Htseq-count Vs CountOverlap function in IRanges biofreak General 5 06-29-2011 10:36 AM
Raw readcounts for RNAseq data using CountOverlaps function in IRanges biofreak General 1 06-28-2011 01:32 PM

Thread Tools
Old 01-26-2012, 01:31 AM   #1
Junior Member
Location: Hyderbad, India

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

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.
Kumar10 is offline   Reply With Quote
Old 01-26-2012, 03:00 PM   #2
Senior Member
Location: Sydney, Australia

Join Date: Jun 2011
Posts: 166


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.

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

    start end width
[1]    10  15     6 [2 2 2 2 2 2]
Dario1984 is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 07:37 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO