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)
this is the error:
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
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!