cghMCR bug?
1
0
Entering edit mode
Ramon Diaz ★ 1.1k
@ramon-diaz-159
Last seen 7.1 years ago
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. -- Ram?n D?az-Uriarte Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez 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) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en s...{{dropped}}
Cancer DNAcopy cghMCR Cancer DNAcopy cghMCR • 470 views
ADD COMMENT
0
Entering edit mode
John Zhang ★ 2.9k
@john-zhang-6
Last seen 7.1 years ago
> >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. > > >-- >Ram?n D?az-Uriarte >Centro Nacional de Investigaciones Oncol?gicas (CNIO) >(Spanish National Cancer Center) >Melchor Fern?ndez 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) > > > >**NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en s...{{dropped}} > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENT

Login before adding your answer.

Traffic: 271 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6