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neurogenomics / EpiCompare

Comparison, benchmarking & QC of epigenetic datasets
https://doi.org/doi:10.18129/B9.bioc.EpiCompare
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Require `TxDb.Hsapiens.UCSC.**.knownGene` #62

Closed bschilder closed 2 years ago

bschilder commented 2 years ago

It looks like TxDb.Hsapiens.UCSC.hg19.knownGene or TxDb.Hsapiens.UCSC.hg38.knownGene is always used. https://github.com/neurogenomics/EpiCompare/blob/2b84d5eba23aec7ca6c5db1bfbd27e4d1606dc29/inst/markdown/EpiCompare.Rmd#L66

Either way, there should be a check at the beginning of the function that ensures the necessary reference is installed. This means that users will find out immediately whether the function call will fail due to one of these not being installed (rather than getting partway through the pipeline).

bschilder commented 2 years ago

Implemented as check_genome_build