I am trying to find overlap between chicken (galGal4) repeat masker file (.rmsk), and promoter region (10k upstream) in the chicken genome, but I got the following warning in r.
Warning message:
In .Seqinfo.mergexy(x, y) :
Each of the 2 combined objects has sequence levels not in the other:
- in 'x': chr11_AADN03010434_random, chr14_AADN03010576_random, chr14_AADN03010579_random, chr14_AADN03010588_random, chr
What I understand there is a difference between both files. Could someone please help me with this warning?
1 answer
It means that the chromosome names in the two different objects on which you are applying findOverlaps() do not match. In general, you can probably ignore the warning as long as you understand that there will be no overlaps on chromosomes in one object but not the other.
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written
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Sean Davis
A warning typically means that R did the work that it thought you wanted and returned a result. You will need to check your results to make sure that R did what you wanted, though. In this case, overlaps were only done on chromosomes available in BOTH objects. As long as you are fine with that, then everything should be OK to proceed.
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written
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Sean Davis
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