Question: Error using singlecn.mops for cnv detection in WGS data
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gravatar for frez111
11 days ago by
frez1110
frez1110 wrote:

Hello,

I am using cnMOPS for Exome cnv analyse which is working fine, since i have multiple samples. However i want to use the function singlecn.mops to detect cnvs in WGS data, where i only have one sample. Unfortunatly i get an Error message:

Starting segmentation algorithm...
Using "fastseg" for segmentation.
Error in checkForRemoteErrors(val) :
one node produced an error: missing value, where TRUE/FALSE needed.
In addition: Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 1 out-of-bound range located on sequence chrMT. Note that ranges located on a sequence
whose length is unknown (NA) or on a circular sequence are not 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 valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 1 out-of-bound range located on sequence chrMT. Note that ranges located on a sequence
whose length is unknown (NA) or on a circular sequence are not 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.

My code looks like this:

#
library(cn.mops)

bams = "*******.bam"

bam_counts = getReadCountsFromBAM(bams, parallel=2)

res = singlecn.mops(bam_counts, parallel=2)

final_genome_cnv = calcIntegerCopyNumbers(res)
#

Do you have any suggestions what i am doing wrong? Thanks in Advance!

cn.mops cnv singlecn.mops • 51 views
ADD COMMENTlink written 11 days ago by frez1110
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