Entering edit mode
8.8 years ago
Hi.
So I am working on a GRangesList, created from a data.frame into GRanges object (S4 class).
The information is repetitive elements and I wish to learn more about identifying 'circular' elements on the chromosome. I received a warning message , that some elements are filtered due their NA values relating to their non-circular flag.
An example element is
1871027 chr16_KI270728v1_random 29112 29357 - BSR/Beta Satellite
and
1875709 chr16_KI270853v1_alt 956887 961336 - SATR2 Satellite
1878449 chr16_KI270853v1_alt 1882350 1886782 + SATR2 Satellite
where these have strange chromosomal names.
There is a function isCircular()
, but how to know which to flag? And why?
Thank you for any useful resources.
Here is my Genomic Ranges object with "NA" entries that is flagged for a warning
Seqinfo object with 455 sequences (1 circular) from 2 genomes (hg19, NA):
seqnames seqlengths isCircular genome
chr1 249250621 FALSE hg19
chr2 243199373 FALSE hg19
chr3 198022430 FALSE hg19
chr4 191154276 FALSE hg19
chr5 180915260 FALSE hg19
... ... ... ...
chrUn_KI270753v1 <NA> <NA> <NA>
chrUn_KI270754v1 <NA> <NA> <NA>
chrUn_KI270755v1 <NA> <NA> <NA>
chrUn_KI270756v1 <NA> <NA> <NA>
chrUn_KI270757v1 <NA> <NA> <NA>