Question: Error from calcIntegerCopyNumbers
0
gravatar for xiaolishimail
5.6 years ago by
China
xiaolishimail0 wrote:

I am trying to use cn.mops for Whole Exome Sequencing with
paired-reads through running the following code:

res_calCNMOPS <- calcIntegerCopyNumbers(resCNMOPS)

and get error message like this,

Error in `[[<-`(`*tmp*`, name, value = c("CN0", "CN0", "CN0", "CN0", "CN0",  :
  367 elements in value to replace 365 elements
 

The complete code I used is here:

>library(cn.mops)
>BAMFiles <- c("tumor_hg19.sorted.bam","normal_hg19.sorted.bam")
>BAIFiles <- c("tumor_hg19.sorted.bam.bai","normal_hg19.sorted.bam.bai")
>segments <- read.delim("~/hg19.bed",sep="\t",header=FALSE,as.is=TRUE)
>gr <- GRanges(segments[,1],IRanges(segments[,2],segments[,3]))

>X <- getSegmentReadCountsFromBAM(BAMFiles,GR=gr,mode="paired")

This may take a couple of minutes per BAM file.Please be patient.


Processing tumor_hg19.sorted.bam
Processing normal_hg19.sorted.bam
 

>resCNMOPS <- exomecn.mops(X,I = c(0.025, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4),classes = c("CN0", "CN1", "CN2", "CN3", "CN4", "CN5", "CN6", "CN7", "CN8"))

Normalizing...
Starting local modeling, please be patient... 
Reference sequence:  chr1
Reference sequence:  chr2
Reference sequence:  chr3
Reference sequence:  chr4
Reference sequence:  chr5
Reference sequence:  chr6
Reference sequence:  chr7
Reference sequence:  chr8
Reference sequence:  chr9
Reference sequence:  chrM
Reference sequence:  chrX
Reference sequence:  chrY
Reference sequence:  chr10
Reference sequence:  chr11
Reference sequence:  chr12
Reference sequence:  chr13
Reference sequence:  chr14
Reference sequence:  chr15
Reference sequence:  chr16
Reference sequence:  chr17
Reference sequence:  chr18
Reference sequence:  chr19
Reference sequence:  chr20
Reference sequence:  chr21
Reference sequence:  chr22
Starting segmentation algorithm...
Using "fastseg" for segmentation.
 

>res_calCNMOPS <- calcIntegerCopyNumbers(resCNMOPS)

Error in `[[<-`(`*tmp*`, name, value = c("CN0", "CN0", "CN0", "CN0", "CN0",  :
  367 elements in value to replace 365 elements
 

The R, cn.mops and Rsamtools packages had been upgraded to the latest version. I tried many tumor and normal paired files and got the similar error message.

 

Could any one please help me with this?

 

snp next-gen • 1.5k views
ADD COMMENTlink modified 5.1 years ago by klambauer20 • written 5.6 years ago by xiaolishimail0
0
gravatar for klambauer
5.1 years ago by
klambauer20
Austria
klambauer20 wrote:

Dear Xiaolishi,
 

I am the author of the package and I am happy to help with the bug. Please contact me via email: klambauer@bioinf.jku.at  and send me your read count matrix such that I am able to reproduce the error.

 

Regards,

Günter Klambauer

ADD COMMENTlink written 5.1 years ago by klambauer20
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