Question about deepSNV warning
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Asma rabe ▴ 290
@asma-rabe-4697
Last seen 6.4 years ago
Japan

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.

 

deepsnv • 1.2k views
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Entering edit mode
@moritzgerstung-9326
Last seen 8.5 years ago
United States

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

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Entering edit mode
Asma rabe ▴ 290
@asma-rabe-4697
Last seen 6.4 years ago
Japan

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

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