txdb object for hg38 for CpG island, CpG shores, Shelves

Question

[Ankit]

Hi everyone,

Does anyone has prior experience of making txdb from gRanges?

I specifically need to create one for CpG island, CpG shores, Shelves (as it is not covered by txdb available).

I tried to make with gRanges and UCSC table but could not do so.

I also tried to make it as follows:

Coordinates of CpG island, CpG shores, Shelves for hg38 version I obtained from build_annotations function which has pre-compiled repository.

annots = c('hg38_cpgs', 'hg38_basicgenes', 'hg38_genes_intergenic',
               'hg38_genes_intronexonboundaries')

annotations = build_annotations(genome = 'hg38', annotations = annots)

txdb_customhg38 <- makeTxDbFromGRanges(annotations)

But still the output txdb_customhg38 does not have the values as keys(txdb_customhg38) print nothing.

keys(txdb_customhg38)
character(0)

Any suggestions how do it if it is possible in R or UNIX?

Thank you

[Ankit]

Any suggestions?