[Bioc-sig-seq] The "ranges" slot in the sread slot of an AlignedRead class

[Nicolas Delhomme]

Hi all,

Well the question is quite easy :-) What does this slot holds? Because  
it looks very different from the actual positions: i.e.

these are the 10 first ranges

 > sread(aln.clean[chromosome(aln.clean)=="2R"])@ranges[1:10]
IRanges object:
      start  end width
[1]   4141 4176    36
[2]   4177 4212    36
[3]   4357 4392    36
[4]   4465 4500    36
[5]   5113 5148    36
[6]   5365 5400    36
[7]   5401 5436    36
[8]   6049 6084    36
[9]   6301 6336    36
[10]  6373 6408    36

and these are the 10 first positions

 >position(aln.clean[chromosome(aln.clean)=="2R"])[1:10]
  [1]  6419544 18694365 10064416 17228214  5850736 11976428 15335440   
3370962
  [9] 15327509  3366816

 > sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE 
= 
en_US 
.UTF 
-8 
;LC_NUMERIC 
= 
C 
;LC_TIME 
= 
en_US 
.UTF 
-8 
;LC_COLLATE 
= 
en_US 
.UTF 
-8 
;LC_MONETARY 
= 
C 
;LC_MESSAGES 
= 
en_US 
.UTF 
-8 
;LC_PAPER 
= 
en_US 
.UTF 
-8 
;LC_NAME 
= 
C 
;LC_ADDRESS 
=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] ShortRead_1.2.0   lattice_0.17-22   BSgenome_1.12.0    
Biostrings_2.12.1
[5] IRanges_1.2.1     rtracklayer_1.4.0 RCurl_0.94-1

loaded via a namespace (and not attached):
[1] Biobase_2.4.1 grid_2.9.0    hwriter_1.1   tools_2.9.0   XML_2.3-0

And is there an easy way to create a RangesList from an AlignedRead  
object? I figured out how to do it, but I just want to be sure that I  
didn't miss it. If it doesn't exist, I think it would be a valuable  
addition and I could contribute the few lines of code.

Best,

---------------------------------------------------------------
Nicolas Delhomme

High Throughput Functional Genomics Center

European Molecular Biology Laboratory

Tel: +49 6221 387 8426
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany