Error in calcCombCnvProb

[Rongtingting]

Hi Prof. Fan, Thank you for your development of HoneyBADGER! I tried hb$retestIdentifiedCnvs(retestBoundGenes=TRUE, retestBoundSnps=TRUE, verbose=FALSE) and get the error: Error in as.vector(x) : no method for coercing this S4 class to a vector I guess there can be something wrong in the calcCombCnvProb method, but I have no idea which step can call this error. Could you help to give some instructions and help to solve the problem?

Thanks a lot!

Best regards, Rongting

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and part of the log:

Aggregating data to list ... Initializing model ... ...Done!restricting to 538 genes in region Aggregating data to list ... Initializing model ... ...Done!restricting to 1341 genes in region Aggregating data to list ... Initializing model ... ...Done!restricting to 443 genes in region Aggregating data to list ... Initializing model ... ...Done!restricting to 192 genes in region Aggregating data to list ... Initializing model ... ...Done!Retesting bound snps ... Assessing posterior probability of CNV in region ... with 1433 snps ... within 290 genes ... converting to multi-dimensional arrays ... Aggregating data to list ... Running model ... Done modeling!WARNING! ONLY 4 SNPS IN REGION! Assessing posterior probability of CNV in region ... with 4 snps ... within 2 genes ... converting to multi-dimensional arrays ... Aggregating data to list ... Running model ... Done modeling!Retesting bound snps and genes using joint modelError in as.vector(x) : no method for coercing this S4 class to a vector Calls: -> union -> unique -> as.vector Execution halted

[Rongtingting]

https://bioinformatics.stackexchange.com/questions/7010/error-in-as-vectorx-no-method-for-coercing-this-s4-class-to-a-vector

and can this be helpful?