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

[Ian Roberts]

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