Warning message in findOverlap function in R

Question

[M K]

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?

Answer 1

[Sean Davis]

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.

[M K]

So that will not effect the results. BTW I downloaded the repeatmasker file from UCSC website and also download the 10k upstream file from UCSC but I used Ensemble Genes from the track tab.

[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.