[BioC] cghMCR bug?

[Ramon Diaz-Uriarte]

Dear All,

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.


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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