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GeneRanges/TXDB formats for annotation? #43

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fruce-ki opened this issue Feb 14, 2018 · 3 comments
Closed
3 tasks done

GeneRanges/TXDB formats for annotation? #43

fruce-ki opened this issue Feb 14, 2018 · 3 comments
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@fruce-ki
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feature request Suggestions for extended functionality. low urgency Does not require immediate attention.
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0.7.0

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fruce-ki commented Feb 14, 2018 •
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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.

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

  • Convert the internal GTF parser to rely on rtracklayer and GenomicRanges?

  • Granges would be useful for plotting gene models (see Plot gene models #44)
@fruce-ki fruce-ki added the feature request Suggestions for extended functionality. label Feb 14, 2018
@fruce-ki fruce-ki self-assigned this Feb 14, 2018
@fruce-ki fruce-ki changed the title GenerRanges/TXDB formats for annotation? GeneRanges/TXDB formats for annotation? Feb 14, 2018
@fruce-ki fruce-ki added the enhancement Suggestions for better performance or better presentation. label Feb 14, 2018
@fruce-ki fruce-ki added this to the 0.7.0 milestone Feb 15, 2018
@fruce-ki fruce-ki removed the enhancement Suggestions for better performance or better presentation. label Feb 19, 2018
@fruce-ki fruce-ki added the low urgency Does not require immediate attention. label May 2, 2018
fruce-ki added a commit that referenced this issue Oct 10, 2018
@fruce-ki
Converted annot2ids() to using rtracklayer::import(). GTF only. Disab…
ded37e4 
…led GFF3 for annot2models() due to ugly behaviour. #44 #43
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fruce-ki commented Oct 10, 2018 •
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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 fruce-ki added the in progress Issue is actively being addressed label Oct 10, 2018
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Extraction of gene/transcript ID pairs from a TxDb seems too simple to warrant a function. Added to vignette.

@fruce-ki fruce-ki removed the in progress Issue is actively being addressed label Jan 14, 2019
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fruce-ki commented Feb 4, 2019

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

@fruce-ki fruce-ki closed this as completed Feb 4, 2019
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