Question: cn.MOPs issue with "Error in if (all(segMedianT == 0))"
gravatar for martyferr90
17 months ago by
martyferr9020 wrote:

Hi all! I'm using cn.MOPs package, but, in the last step, I have an error message. This are my steps:

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

> bDR<-getReadCountsFromBAM(BAMFiles)

> res<-cn.mops(bDR)

but this is my output:


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:  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

Reference sequence:  chrX

Reference sequence:  chrY

Reference sequence:  chrM

Starting segmentation algorithm...

Using "fastseg" for segmentation.

Error in if (all(segMedianT == 0)) { :

  missing value where is request TRUE/FALSE

Inoltre: Warning messages:

1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :

  GRanges object contains 1 out-of-bound range located on sequence chrM.

  Note that only ranges located on a non-circular sequence whose length

  is not NA can be considered out-of-bound (use seqlengths() and

  isCircular() to get the lengths and circularity flags of the underlying

  sequences). You can use trim() to trim these ranges. See

  ?trim,GenomicRanges-method for more information.

2: In normalizeChromosomes(X, chr = chr, normType = normType, qu = normQu,  :

  Normalization for reference sequence  chrM not applicable, because of low number of segments


Is there something that I miss?

I use R-patched 3.4.2 with --vanilla on Ubuntu 17.10

Thank you for your help!

cn.mops cnv • 402 views
ADD COMMENTlink modified 17 months ago by Günter Klambauer540 • written 17 months ago by martyferr9020
Answer: cn.MOPs issue with "Error in if (all(segMedianT == 0))"
gravatar for Günter Klambauer
17 months ago by
Günter Klambauer540 wrote:

There seems to be some problem with the read counts. Can you check the distributions of read counts (the values in your object "bDR"), such as mean, median, max, number of zeros, NAs?

ADD COMMENTlink modified 17 months ago • written 17 months ago by Günter Klambauer540

having exactly the same issue/error as the above poster.  What was the solution here?  Thanks for posting a follow-up to this query as I suspect others may be having this issue.

ADD REPLYlink written 12 months ago by daniel.waller0
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