Target GPos when computing coverage

tidyomics / plyranges

A grammar of genomic data transformation

https://tidyomics.github.io/plyranges/

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Target GPos when computing coverage #66

Open lawremi opened 5 years ago

lawremi commented 5 years ago

It's common to want base-level (not run level) coverage from a GRanges object. It could be stored in a GPos, which behaves just like a GRanges, except there is a feature per base. Maybe the function could be named compute_baselevel_coverage()?

sa-lee commented 5 years ago

Sorry for taking so long to respond to this - I was keen to use GPos for some other analyses I was doing but found that large genomes were problematic so you couldn't have long-form tables that plyranges expects. I guess your proposed function could throw an error in this case?