cghMCR package:Is it possible to find MCR by not usingDNAcopy object?
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viritha kaza ▴ 580
Last seen 8.0 years ago
Hi John, Thanks for your reply. I saw 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:"" 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 <> 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: > [] 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]] > > _______________________________________________ > Bioconductor mailing list > > > Search the archives: > > > > > The information in this e-mail is intended only for th...{{dropped:17}}
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