[BioC] cghMCR bug?

[John Zhang]

>
>I am trying to run cghMCR on several objects from DNAcopy, but I keep getting 
>an error that says  
>
>Error in data.frame(span = "span.1", loc.end.loc.end = numeric(0), check.names 
>= TRUE,  : 
>        arguments imply differing number of rows: 1, 0
>
>I think this happens whenever the settings would lead to no segments selected 
>(i.e., the error disappears if we are more liberal with alteredLow and 
>alteredHigh). I do not really understand what the code is doing, but I think 
>it should return an empty object (and possibly a warning), not crash with an 
>error.


I will have a look at the code. Thanks for reporting.


>
>
>This behavior is easy to reproduce with the vignnette data (no, it is not due 
>to repeated maplocs)
>
>require(cghMCR)
>data("sampleData")
>segments <- getSegments(sampleData)
>cghmcr2 <- cghMCR(segments, gapAllowed = 500, alteredLow = 0.001, 
>		alteredHigh = 0.999, recurrence = 50)
>mcrs2 <- MCR(cghmcr2)
>
>
>Best,
>
>R.
>
>
>-- 
>Ramón Díaz-Uriarte
>Centro Nacional de Investigaciones Oncológicas (CNIO)
>(Spanish National Cancer Center)
>Melchor Fernández Almagro, 3
>28029 Madrid (Spain)
>Fax: +-34-91-224-6972
>Phone: +-34-91-224-6900
>
>http://ligarto.org/rdiaz
>PGP KeyID: 0xE89B3462
>(http://ligarto.org/rdiaz/0xE89B3462.asc)
>
>
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084