[BioC] snapCGH; export results of summarize.clones() function from aCGH

[Steven McKinney]

Hi Ian,

I looked at older versions of snapCGH, and
indeed version 1.1.0 had a function
summarizeClones()
which has indeed disappeared :(

I do not see a straightforward way of
converting a SegList object to an aCGH type
object, I'm not up to date on the definitions
of the various components of snapCGH's SegList 
and aCGH objects.  For example, summarize.clones()
seems to work with kb units for clone positions
but snapCGH works with Mb units so some care
is needed to convert objects.

Output for snapCGH at present appears to
be all graphical.

The function nudSegmentation() in snapCGH appears to
generate the type of data from which output similar 
to that from summarize.clones() could be obtained
(see the "regions" component of nudSegmentation
output). 

Mike and John - do you have any plans to implement
a function like the old summarizeClones() function
to produce output similar to summarize.clones()
for SegList objects? 


Steven McKinney

Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney at bccrc.ca

tel: 604-675-8000 x7561

BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C. 
V5Z 1L3
Canada




-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch on behalf of Ian Roberts
Sent: Tue 6/26/2007 12:52 AM
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC]snapCGH;	export results of summarize.clones() function from aCGH
 
Steven McKinney <smckinney at ...> writes:

> 
> Hi Ian,
> 
> On 25 Jun 2007, at 11:58, Ian Roberts wrote:
> 
> >
> >
> > I've got snapCGH set up and running well - and drawing all the  
> > plots I need.  However I am struggling to export a list of clones  
> > from the summarize.clones function.  That is, a list of  clones  
> > present in the segmented regions of the genome across all samples  
> > contained in the SegInfo object.  I am sure a function was  
> > available in earlier snapCGH versions 'export clones' but doesn't  
> > seem to be there now?
> >
> > Thanks for your help.
> >
> >
> >
> > Ian

> 
> Using the latest version of snapCGH() installed with
> biocLite(), I see that the current version of the
> function summarize.clones() returns a data frame
> of results.  
> 
> (Note also that summarize.clones() is in the
> package "aCGH" that snapCGH loads.)
> 
> The return clause of the function
> is wrapped with "invisible()" so you won't
> see the returned data frame if you invoke the
> command in an interactive R session.
> 
> The help page for summarize.clones() shows
> a basic example
> 
> data(colorectal)
> summarize.clones(colorectal)
> 
> You can capture the resultant
> data frame into a user variable, e.g.
> 
> foo <- summarize.clones(colorectal)
> 
> Object "foo" will be a data frame that
> you can view, or export to an external
> file using write.table() or write.csv().
> 
> Or you can just output the results of
> summarize.clones() directly, e.g.
> 
> write.csv(summarize.clones(colorectal), file = "colo.clone.summary.csv")
> 

> 
Dear Steven,

Thanks very much for your reply.  Unfortunately being an R newbie, and still 
relatively unfamiliar with snapCGH and aCGG packatges I've been unable to get 
your suggestion working.

Effectively, snapCGH ends up with a SegList (e.g. SegInfo.Bio.merge) that 
contains the required information.  SegList is An object of class "SegList"

I see that summarize.clones is an aCGH function that takes aCGH.objects as 
targets.  Consequently if I do:

> results<-summarize.clones(SegInfo.Bio.merge)
I get ...
Error in rep(posThres, ncol(dat)) : invalid 'times' argument

... and I have no idea what that means.

I suspect there is some easy method to convert SegLists to aCGH objects, and 
would appreciate any help available in that regard.

Thanks for your assistance.
Best wishes,

Ian

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