[BioC] cghMCR package:Is it possible to find MCR by not usingDNAcopy object?

[Jianhua Zhang]

Hi, Viritha,

The SGOL approach takes a segment list object and is a better alternative to
the MCR approach. If you read the latest version of cghMCR, there is a
section showing the steps to take.

If you would want to make a DNAcopy object off a segment list, you first
make a list with three elements (I remember it is something like data,
output or out, and call. Output or out contains the seglist) and then make
it a DNAcopy class.

Hope this help.



John




-----Original Message-----
From: bioconductor-bounces at r-project.org
[mailto:bioconductor-bounces at r-project.org] On Behalf Of viritha k
Sent: Thursday, September 29, 2011 4:40 PM
To: Bioconductor; Hervé Pagès
Subject: [BioC] cghMCR package:Is it possible to find MCR by not
usingDNAcopy object?

Dear Group,
I saw this question asked but did not find a reply and I have the same
question.
I was looking for a package that provides functions to identify minimum
common genomic regions of interests based on segmented copy number data from
multiple samples. I've found cghMCR package could be very useful for me.
The Manual shows how to generate the segment data based on raw data using
DNAcopy package, and then, use these segment data (as a DNAcopy class
object)  as the input to the cghMCR function. My problem is I've generated
the segment list using other method. This segment list has the same
parameters:
1)the sample id,
2)the chromosome number,
3)the map position of the start of the segment,
4)the map position of the end of the segment,
5)the number of markers in the segment
6)the average value in the segment
but it is a data frame object, not a DNAcopy object like "segData".
How could I apply cghMCR and MCR functions using my R data frame? Is there
some method to get a DNAcopy class object from my segment list?

Thanks,
Viritha

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