GeneRanges/TXDB formats for annotation?

fruce-ki commented 6 years ago

Make RATs more friendly towards Bioconductor by allowing users to supply their annotation in established Bioconductor formats, such as GRanges or TxDb. Either format should be simple to convert to a list of transcript and gene IDs, but currently users have to do this themselves. If we aim to submit RATs to Bioconductor, RATs should become compatible with the Bioconductor structures directly.

[x] helper function(s) to create transcript-to-gene look-up table from a TxDb or from a GRanges representation of a GTF/GFF3.

[x] Convert the internal GTF parser to rely on rtracklayer and GenomicRanges?
[x] Granges would be useful for plotting gene models (see #44)

fruce-ki commented 5 years ago

Pairing the gene and transcript IDs in a 2xN table is more complex starting from GFF3-derived GRanges, because the Parent column is a list of lists, making it difficult to match the values in them to find the transcripts. Further investigation need...

TxDb compatibility not explored yet.

fruce-ki commented 5 years ago

Extraction of gene/transcript ID pairs from a TxDb seems too simple to warrant a function. Added to vignette.

fruce-ki commented 5 years ago

Trying to figure out why this issue was not closed. The action points have been addressed, so what's missing?

bartongroup / RATS

GeneRanges/TXDB formats for annotation? #43