Sorry, that's actually easier than that for defining the indices. I
got confused by playing with them back and forth between the different
objects. This (really) does the job:
mrna.ranges<-RangedData(
IRanges(start=position(mrna.aln),width=width(mrna.aln)),
space = chromosome(mrna.aln),
universe = "dm3",
indices=seq(along=mrna.aln)
)
Have a nice WE,
---------------------------------------------------------------
Nicolas Delhomme
High Throughput Functional Genomics Center
European Molecular Biology Laboratory
Tel: +49 6221 387 8426
Email: [email protected]
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------
On 15 May 2009, at 15:04, Martin Morgan wrote:
Thanks Nicolas, that looks tidier! I'll talk to Michael a little to
make sure I understand everything, and then implement this probably as
a constructor (instead of coerce). Will let you; it might not be till
next week. Martin
Nicolas Delhomme <[email protected]> writes:
Hi Martin, Hi all,
The following code does what I want quite nicely:
mrna.ranges<-RangedData(
IRanges(start=position(mrna.aln),width=width(mrna.aln)),
space = chromosome(mrna.aln),
universe = "dm3",
indices=unlist(sapply(levels(chromosome(mrna.aln)),function(chr)
{which(chromosome(mrna.aln)==chr)}),use.name=FALSE)
)
Out of my AlignedRead (mrna.aln), I create a RangedData which
contains
the ranges splitted by chromosome and sorted into a RangesList. The
additional parameter: indices (the name is arbitrary) contains the
position of the corresponding read in the original mrna.aln object
and
is stored in a SplitXDataFrame.
Best,
---------------------------------------------------------------
Nicolas Delhomme
High Throughput Functional Genomics Center
European Molecular Biology Laboratory
Tel: +49 6221 387 8426
Email: [email protected]
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------
On 13 May 2009, at 16:53, Martin Morgan wrote:
Nicolas Delhomme <[email protected]> writes:
Hi Martin,
That's what I thought; i was just curious to learn more. Thanks for
the details!
I should have think of it, as I put it after the session info, that
most probably my second question will be invisible :-)
I paste it here again:
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.
Sorry for missing that; I don't think there is anything built-in. We
could exchange your code about introducing something off-list, if
you
like.
Martin
Best wishes,
---------------------------------------------------------------
Nicolas Delhomme
High Throughput Functional Genomics Center
European Molecular Biology Laboratory
Tel: +49 6221 387 8426
Email: [email protected]
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------
On 13 May 2009, at 04:30, Martin Morgan wrote:
Hi Nicolas --
Nicolas Delhomme <[email protected]> writes:
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]
It's internal to the way reads themselves are stored.
sread(aln.clean)
returns a DNAStringSet object, the ranges slot of a DNAStringSet
points to offsets into a larger DNAString. As you show later, you
want to use position(aln.clean) for alignment information.
This representation is meant to be entirely internal to the class.
The
intention is that the user manipulate objects with defined
functions
and methods (like position()). Of course the user can get at the
contents of slots with @, but there are no guarantees about what
will
be there if the user does this!.
Martin
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: [email protected]
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
