txdb object for hg38 for CpG island, CpG shores, Shelves
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.
Any suggestions how do it if it is possible in R or UNIX?
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