Hi John,

Thanks for your reply.

I saw http://rss.acs.unt.edu/Rdoc/library/cghMCR/html/cghMCR.html

here that

*Usage*:

cghMCR(segments, gapAllowed = 500, alteredLow = 0.03, alteredHigh =

0.97, spanLimit = 2e+07, recurrence = 75)

*Arguments*

segments

:segments is a data frame extracted from the "output" element of the object
returned by segment of the package DNAcopy or
getSegments<http://rss.acs.unt.edu/Rdoc/library/cghMCR/html/cghMCR-class.html>
.

In other places I see as you mentioned that results from the segmentation
analysis (segments) is a list with three elements:

> names(segments)

[1] "data" "output" "call"

*Results of segmenting a CNA data object*

data



The original CNA object which was the input for segment

ID

sample identifier.

chrom

the chromosome within the sample.

loc.start

the starting map location of the segment

loc.end

the ending map location of the segment

num.mark

the number of markers in the segment

data.type

the segment mean.

call

the call that produced the object.



So I am little confused if I need to use cghMCR to identify minimum common
regions I would need to construct CNA data object with call. Is there any
alternative to this rather than going by the whole process and getting the
original CNA object and call?


On Fri, Sep 30, 2011 at 8:48 AM, Jianhua Zhang <
jianhua_zhang@dfci.harvard.edu> wrote:

> 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@r-project.org
> [mailto:bioconductor-bounces@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
>
>        [[alternative HTML version deleted]]
>
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