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JEFworks-Lab / HoneyBADGER

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
http://jef.works/HoneyBADGER/
GNU General Public License v3.0
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lt$setGexpDev #28

Closed BoXiaHB closed 5 years ago

BoXiaHB commented 5 years ago

I am experiencing problem while executing the setGexpDev function with my data. I think the error might be at the step: gexp.sd <- sd(gexp.norm). The function, in standalone setting, works when I convert the gexp.norm into a matrix.

lt$setMvFit(verbose=TRUE) Modeling expected variance ... Done! lt$setGexpDev(verbose=TRUE) Error in is.data.frame(x) : (list) object cannot be coerced to type 'double' setGexpDev(as.matrix(lt$gexp.norm)) 1 0.1507096 lt$calcGexpCnvBoundaries(init=TRUE, verbose=FALSE) Error in -dev : invalid argument to unary operator

BoXiaHB commented 5 years ago

Solution: gexp should be a data matrix, and not a dataframe