cghMCR package:Is it possible to find MCR by not using DNAcopy object?
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viritha kaza ▴ 580
@viritha-kaza-4318
Last seen 7.1 years ago
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]]
DNAcopy cghMCR DNAcopy cghMCR • 854 views
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@jianhua-zhang-4191
Last seen 7.1 years ago
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 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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor The information in this e-mail is intended only for the ...{{dropped:11}}
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