Entering edit mode
I am using rtracklayer to import bedpe but had an error:
what's wrong? thanks! There are no empty lines in the file.
cat -A test.bedpe chr1^I100^I200^Ichr5^I5000^I5100^Ibedpe_example1^I30^I+^I-$ chr9^I1000^I5000^Ichr9^I3000^I3800^Ibedpe_example2^I100^I+^I-$ import("test.bedpe", format="bedpe") Error in validObject(.Object) : invalid class “GRanges” object: 'seqnames(x)' contains missing values
Actually, this might be a real bug. It seems that a
seqinfo
object somewhere is defined from the first set of chromosomes (chr1
andchr9
), so that when it comes to load the second set ofGRanges
, thechr5
entry ends up being a missing value. I can reproduce the error message in the original post, and I can get it to go away by changingchr5
tochr1
.good to know you can reproduce the error. Thx.
Thanks for pointing that out, updated answer.