Question

cn.mops returning only "NA" as copy number

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rc16955 • 0

@rc16955-12563

Last seen 7.7 years ago

Dear all,

I've been trying to use cn.mops to identify copy number variants among 10 individual of my (non-human) study species. Each individual was subjected to Illumina whole-genome sequencing, and the reads were mapped to the reference using Bowtie2. I have mostly been following the cn.mops manual:

>BAMFiles<-list.files(pattern=".bam$")

>bamDataRanges<-getReadCountsFromBAM(BAMFiles,sampleNames=paste("sample",1:10),mode="paired")

>resCNMOPS<-cn.mops(bamDataRanges)

All of this went through without error. However, when I try to view the data (with cnvs or cnvr), everything in the "logical" column, which I believe should contain the estimates for copy number simply says "<NA>" What could be the cause of this?

I am able to view plots of the data with plot and segplot just fine.

Thank you

cn.mops • 1.2k views

ADD COMMENT • link updated 7.7 years ago by Günter Klambauer ▴ 540 • written 7.7 years ago by rc16955 • 0

score 0 · Answer 1 · 2017-03-13

This is the default behaviour. The function "calcIntegerCopyNumbers" replaces the NA values with integer copy numbers. Regards, Günter On 2017-03-11 00:15, rc16955 [bioc] wrote: > Activity on a post you are following on support.bioconductor.org > <https: support.bioconductor.org=""> > > User rc16955 <https: support.bioconductor.org="" u="" 12563=""/> wrote > Question: cn.mops returning only "NA" as copy number > <https: support.bioconductor.org="" p="" 93721=""/>: > > Dear all, > > I've been trying to use cn.mops to identify copy number variants among > 10 individual of my (non-human) study species. Each individual was > subjected to Illumina whole-genome sequencing, and the reads were > mapped to the reference using Bowtie2. I have mostly been following > the cn.mops manual: > > >BAMFiles<-list.files(pattern=".bam$") > > >bamDataRanges<-getReadCountsFromBAM(BAMFiles,sampleNames=paste("sample",1:10),mode="paired") > > >resCNMOPS<-cn.mops(bamDataRanges) > > All of this went through without error. However, when I try to view > the data (with cnvs or cnvr), everything in the "logical" column, > which I believe should contain the estimates for copy number simply > says "<na>" What could be the cause of this? > > I am able to view plots of the data with plot and segplot just fine. > > Thank you > > ------------------------------------------------------------------------ > > Post tags: cn.mops > > You may reply via email or visit > cn.mops returning only "NA" as copy number > -- Günter Klambauer, PhD Institute of Bioinformatics Johannes Kepler University, Linz, Austria http://www.bioinf.jku.at/people/klambauer/