In valid.GenomicRanges.seqinfo

[minn333]

Dear:
Could you tell me how I correct the errors?

library(cn.mops)

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

res <- cn.mops(bamDataRanges)

Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 4 out-of-bound ranges located on sequences
chrM, chr18_gl000207_random, chrUn_gl000226, and chrUn_gl000229. 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.

Starting segmentation algorithm...
Using "fastseg" for segmentation.
Error in if (all(segMedianT == 0)) { :
missing value where TRUE/FALSE needed
Calls: cn.mops -> apply -> FUN
In addition: Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 4 out-of-bound ranges located on sequences
chrM, chr18_gl000207_random, chrUn_gl000226, and chrUn_gl000229. 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 normalizeChromosomes(X, chr = chr, normType = normType, qu = normQu, :
Normalization for reference sequence chrM not applicable, because of low number of segments
3: In normalizeChromosomes(X, chr = chr, normType = normType, qu = normQu, :
Normalization for reference sequence chr9_gl000200_random not applicable, because of low number of segments
4: In normalizeChromosomes(X, chr = chr, normType = normType, qu = normQu, :
Normalization for reference sequence chr18_gl000207_random not applicable, because of low number of segments
5: In normalizeChromosomes(X, chr = chr, normType = normType, qu = normQu, :
Normalization for reference sequence chrUn_gl000226 not applicable, because of low number of segments
6: In normalizeChromosomes(X, chr = chr, normType = normType, qu = normQu, :
Normalization for reference sequence chrUn_gl000229 not applicable, because of low number of segments
Execution halted

[vjcitn]

Thanks for your note. Without access to your bam files it is not really possible to give detailed help. However, I did note that the proposed code fails when applied to the example data noted on the README of this repo. I did get success when I added segAlgorithm='DNAcopy' to the cn.mops call.

[minn333]

Hello, I had set refSeqNames to omit the 4 out-of-bound ranges located on sequences
chrM, chr18_gl000207_random, chrUn_gl000226, and chrUn_gl000229. Maybe make sense!

Thanks for your reply!

bamDataRanges <- getReadCountsFromBAM(BAMFiles, refSeqNames=c("chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20","chr21","chr22","chrX","chrY"))