Hi all,

I got this error when i used bf2Vcf function in deepSNV package

counts<-loadAllData(treated,control,regionfile)

BF<-bbb(counts,model="AND")

vcf1<-bf2Vcf(BF=BF,counts=counts,regions=regionfile,samples=files)

Warning message:
In t(round(-10 * log10(pp))) : NaNs produced

Any help is appreciated.

Hi Asma

Can you provide a reproducible example? It seems that for some reason pp has a negative element, hence the NaN in log10(). Are any values in BF negative? It would be interesting to inspect the corresponding counts as well.

Thank you,

Moritz

Hi Moritz,

Thank you for reply, I found that one lament in BF has negative value and it is the reason of warning. Do you know how to fix this and if this warning affect the output.

Thank you.

#=============

treated="treated.bam"

control="control.bam"

regionfile <- GRanges("refrence_region", IRanges(start = 3120, end=3140))

counts<-loadAllData(treated,control,regionfile)

BF<-bbb(counts,model="AND")

vcf1<-bf2Vcf(BF=BF,counts=counts,regions=regionfile,samples=files)

Warning message:
In t(round(-10 * log10(pp))) : NaNs produced