Error using singlecn.mops for cnv detection in WGS data
0
0
Entering edit mode
frez111 • 0
@frez111-22309
Last seen 5.0 years ago

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!

cnv cn.mops singlecn.mops • 993 views
ADD COMMENT
0
Entering edit mode

One way that I used is changing the seqlevels of "bamDataRanges", like this:

temp <- seqlevels(bamDataRanges, pruning.mode="coarse") <- setdiff(seqlevels(bamDataRanges), "chrMT")

seqlevels(bamDataRanges) <- temp

...And you're good to go.

ADD REPLY

Login before adding your answer.

Traffic: 765 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6