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>