[Bioc-sig-seq] AlignedRead and IRanges

James Bullard bullard at berkeley.edu
Thu Aug 6 20:29:42 CEST 2009

I believe that this should be a relatively straightforward thing to  
do, but I am having trouble finding out the best bioC way to perform  
this computation. I have an AlignedRead object from a call to  
readAligned. Additionally I have a set of IRanges (rngs). I want to  
determine the number of reads which are within each range.  
Specifically, I would like a vector of length length(rngs) where each  
element represents the total number of reads within that range.

thanks, jim

ps. I am working with the current release version of R/Bioc

R version 2.9.1 Patched (2009-07-31 r49063)


attached base packages:
[1] grid      stats     graphics
[4] grDevices utils     datasets
[7] methods   base

other attached packages:
  [1] Genominator_1.0.0
  [2] RSQLite_0.7-1
  [3] DBI_0.2-4
  [4] GenomeGraphs_1.4.1
  [5] biomaRt_2.0.0
  [6] ShortRead_1.2.1
  [7] lattice_0.17-25
  [8] BSgenome.Scerevisiae.UCSC.sacCer1_1.3.13
  [9] BSgenome_1.12.2
[10] Biostrings_2.12.7
[11] IRanges_1.2.3

loaded via a namespace (and not attached):
[1] Biobase_2.5.3 hwriter_1.1
[3] RCurl_0.98-1  XML_2.5-1

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