From vmakarov at pace.edu  Thu Feb 21 16:22:14 2008
From: vmakarov at pace.edu (Vladmir Makarov)
Date: Thu, 21 Feb 2008 10:22:14 -0500
Subject: [Rd] DNAcopy package output data
In-Reply-To: <6phzltvcl1i.fsf@gopher4.fhcrc.org>
References: <7cac4bd80802201351i6c5f87fao2e076a47b05c65ed@mail.gmail.com>
	<6phzltvcl1i.fsf@gopher4.fhcrc.org>
Message-ID: <7cac4bd80802210722w6bab51c7lb89a91e4667cf9aa@mail.gmail.com>

>The longer answer is 'yes', since the source of the
> function is readily available (typing segment)

Hello,
That is exactly why I have posted this question at the development
forum - there was no way of specifying output parameters in the
"segment" function
Thank you
Vlad

On 2/20/08, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> This is a Bioconductor package, so please address questions to the
> Bioconductor list (instructions at
> http://www.bioconductor.org/docs/mailList.html). This is not a
> question related to 'development' but to use, so you do not need to
> ask on the '-devel' mailing list.
>
> Do you mean the result of 'segment'? It's always helpful to provide a
> reproducible (e.g., using the example data provided with the package)
> example!
>
> I think the easy answer to your question is 'no', there are no
> documented arguments influencing how statistics on the segment are
> calculated. The longer answer is 'yes', since the source of the
> function is readily available (typing
>
> > segment
>
> ) and the segment boundaries are returned and hence other statistics
> can be calculated by the user.
>
> Hope that helps,
>
> Martin
>
> "Vladmir Makarov" <vmakarov at pace.edu> writes:
>
> > Hello R Developers
> >
> > I am using DNACopy package
> > http://bioconductor.org/packages/1.9/bioc/html/DNAcopy.html
> >
> > I am not able to figure out how to (if at all possible) to modify
> > output format, namely, I am getting the following:
> > "ID"  "chrom" "loc.start"     "loc.end"       "num.mark"      "seg.mean"
> >
> > Is it a way to get also median and standard deviation?
> >
> > Thanks in advance,
> > Vlad
> >
> > --
> > ***********************************
> >  Dr. Vladimir Makarov
> >  Instructor, Computer Science Department
> >  School of Computer Science and Information Systems
> >  Pace University
> >  163 Williams Street
> >  New York, NY 10038
> >  Phone: (212) 639 - 7422
> >  eMail: vmakarov at pace.edu
> >  http://matrix.csis.pace.edu/~vmakarov/
> >
> > ***********************************
> >
> > ####################################################################
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> > ______________________________________________
> > R-devel at r-project.org mailing list
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>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M2 B169
> Phone: (206) 667-2793
>


-- 
***********************************
  Dr. Vladimir Makarov
  Instructor, Computer Science Department
  School of Computer Science and Information Systems
  Pace University
  163 Williams Street
  New York, NY 10038
  Phone: (212) 639 - 7422
  eMail: vmakarov at pace.edu
  http://matrix.csis.pace.edu/~vmakarov/

***********************************

####################################################################
The information contained in this email message and any files
transmitted with it are confidential and intended solely for the use
by the individual(s) originally addressed. Please disregard and delete
this email if you are not the intended recipient.
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[Rd] DNAcopy package output data
Vladmir Makarov