Inconsistent Warning: GRanges out of bounds
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znl207 • 0
@znl207-14983
Last seen 3.5 years ago

Hello: I am observing an error with cnMOPs and wondering if you have any recommendation to fix it. - let me know if I should be directing this message to someone else. 

These are the commands I am running:

CHR=c(chr01 chr02 chr03 chr04 chr05 chr06 chr07 chr08 chr09 chr10 chr11 chr12)

BAMfiles <- list.files(pattern=".bam$", full.names=TRUE, recursive=TRUE)

BAMdataranges <- getReadCountsFromBAM(BAMfiles, Ids, refSeqNames = CHR, WL= 500)

output <- cn.mops(BAMdataranges, minWidth=3, minReadCount=3)

int_output<- calcIntegerCopyNumbers(output)

this is the error: 

"Warning message:

GRanges object contains 591 out-of-bound ranges located on sequences

  chr11, chr02, chr08, and chr09. 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 "

I have tried running this on different sets of chromosomes - there are no errors running the program on chromosomes 1-9, however if it is run on chromosomes 1-10, 1-11, or 1-12 the warning message points to out of bounds ranges on different sets of chromosomes.

Here is a summary of the different results

Chr 1-10: out of bounds chr 9

Chr 1-11: out o f bounds chr 11, 2, 5, 9,

Chr 1-12: out of bounds chr 11, 02, 08, 09 

Do you have an suggestions for how to fix this error? The program does make output files, I have not looked extensively at non-consecutive combinations of chromosomes. 

Thank you for your help!

cn.mops granges trim Genomicranges-method • 501 views
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Hi znl207,

In order for anyone to provide assistance, please post a fully reproducible and

minimal example of the issue.

What I see from the output, it doesn't look like an error but more of a warning.

It could be related to a number of issues including the integrity of the data.

One option you could try is options(warn = 2) and track the source of the warnings

that you're getting.

Best regards,

Marcel

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