From mtmorgan at fhcrc.org  Wed Feb 20 23:36:41 2008
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Wed, 20 Feb 2008 14:36:41 -0800
Subject: [Rd] DNAcopy package output data
In-Reply-To: <7cac4bd80802201351i6c5f87fao2e076a47b05c65ed@mail.gmail.com>
	(Vladmir Makarov's message of "Wed, 20 Feb 2008 16:51:34 -0500")
References: <7cac4bd80802201351i6c5f87fao2e076a47b05c65ed@mail.gmail.com>
Message-ID: <6phzltvcl1i.fsf@gopher4.fhcrc.org>

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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>
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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



[Rd] DNAcopy package output data
Martin Morgan