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Error in if (all(x <= minReadCount) & lambda <= minReadCount) { : missing value where TRUE/FALSE needed

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s1812756 • 0

@s1812756-21082

Last seen 5.4 years ago

Dear Dr Klambauer,

I met an error when using singlecn.mops. At the modelling part, it runs well at the beginning, but when operating on NW_020228985.1, an error occurred as below, but it runs well when I try it using the same reference genome. Will it matter if the reference genome is not in the same directory?

......
Reference sequence:  NW_020228924.1
Reference sequence:  NW_020228957.1
Reference sequence:  NW_020228985.1
Error in if (all(x <= minReadCount) & lambda <= minReadCount) { : 
  missing value where TRUE/FALSE needed
Calls: singlecn.mops -> lapply -> FUN -> .singlecn.mops
Execution halted

Thank you Mengyuan Li

cnmops cn.mops error • 1.1k views

ADD COMMENT • link updated 5.4 years ago by Martin Morgan 25k • written 5.4 years ago by s1812756 • 0

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You have NAs in x probably.

ADD REPLY • link 5.4 years ago asafpr • 0

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Thank you. And, I finally found that problem. The solution is to use "samtools view name.bam | awk '{print $3}' | uniq -c" to get the read count from the BAM file. And use the chromosome names in the second line as refSeqNames parameter

ADD REPLY • link 5.4 years ago s1812756 • 0

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For what it's worth sequence names are available from within R using Rsamtools quickly and easily, for example, after running example(countBam) to get a path to a bam file fl

> seqnames(seqinfo(BamFile(fl)))
[1] "seq1" "seq2"
> idxstatsBam(fl)$seqnames
[1] seq1 seq2
Levels: seq1 seq2
> seqnames(seqinfo(BamFile(fl)))
[1] "seq1" "seq2"

ADD REPLY • link 5.4 years ago Martin Morgan 25k