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Genentech / FacileDataSet

A fluent API for accessing multi-assay high-throughput genomics data.
MIT License
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prefix a few functions #22

Open phaverty opened 5 years ago

phaverty commented 5 years ago

dplyr and data.table have symbol clashes with some other packages. Let's use the namespace prefix ( double colon ) in a few carefully selected places

phaverty commented 5 years ago

Warning: replacing previous import ‘Biobase::samples’ by ‘FacileAnalysis::samples’ when loading ‘FacileDataSet’ Warning: replacing previous import ‘Biobase::anyMissing’ by ‘checkmate::anyMissing’ when loading ‘FacileDataSet’ Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘FacileDataSet’ Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘FacileDataSet’ Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘FacileDataSet’ Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘FacileDataSet’ Warning: replacing previous import ‘data.table::melt’ by ‘reshape2::melt’ when loading ‘FacileDataSet’ Warning: replacing previous import ‘data.table::dcast’ by ‘reshape2::dcast’ when loading ‘FacileDataSet’ Warning: replacing previous import ‘magrittr::extract’ by ‘tidyr::extract’ when loading ‘FacileDataSet’ Warning: replacing previous import ‘FacileAnalysis::samples’ by ‘Biobase::samples’ when loading ‘FacileDataSet’ Warning: replacing previous import ‘FacileAnalysis::organism’ by ‘BiocGenerics::organism’ when loading ‘FacileDataSet’

lianos commented 5 years ago

I'm all for adding prefixes where necessary.

Also, though: recent changes to the codebase are importing things wholesale that shouldn't: for instance, there's no reason to do a wholesale import of Biobase

Further, technically I think things like Biobase, SummarizedExperiment, and other package that provide assay containers should rather be a Suggests thing, no?

phaverty commented 5 years ago

SummarizedExperiment can go in Suggests since we requireNamespace it We need Biobase and BiocGenerics for the generics for organism and samples. I guess we can just import those 2 things. On it ...

phaverty commented 5 years ago

Actually, we already only import 1 thing each from Biobase and BiocGenerics. I wouldn't mind just making organism just an expected field in the top-level metadata. Then we could drop Biobase. If we could tolerate samples_tbl or something, we could drop BiocGenerics.

We can drop SummarizedExperiment when all the as.BioCWhatever moves to FacileData/FacileAnalysis. K?