Changes in response to the second review:
methylTFRAnnotationHg38.datadir option or
METHYL_TFRANNOTATION_HG38_DIR value (not a single string, or a directory
that does not exist) now gives an informative error. Tests
added.inst/extdata/README.md describing metadata.csv and
each AnnotationHub resource.?motif_gcfreq,
?tf_bindsites, ?genomewide_GC) have a \value section, and
their examples run (reading metadata.csv) instead of using
\dontrun.CITATION.cff.Changes in response to the Bioconductor review:
Authors@R lists the funders (ERA-NET Transcan-Neu III - EPILUNAR,
grant 01KT2409; Saarland University NanoBioMed Young Investigator
Grant) with the fnd role.
New package help page ?methylTFRAnnotationHg38 summarising the resources and
linking the accessors.
New help pages describing the structure of each AnnotationHub resource
listed in inst/extdata/metadata.csv: ?motif_gcfreq
(?altius_motif_gcfreq, ...), ?tf_bindsites
(?altius_tf_bindsites, ...) and ?genomewide_GC
(?genomewide_GC_hg38).
New exported availableMotifSets() listing the accepted motif sets.
getGenomeGC() accepts "hg38" (or no argument) and gives an
informative error for any other assembly.
getTFbindsites() accepts _distal set names and returns the
binding sites of the base set.
Unit tests now cover the local-directory and AnnotationHub code paths (the hub is mocked, so the tests run offline).
The vignette no longer hides code: the synthetic example data are built in a visible chunk, every chunk is evaluated, and each accessor's output is printed and explained.
Initial submission to Bioconductor.
Provides transcription factor binding sites, motif GC frequency tables and a genome-wide GC distribution for hg38, for the jaspar2020, cisbpv2 and altius motif sets, plus a distal-restricted GC frequency table for jaspar2020.
Resources are hosted on AnnotationHub and downloaded on first use.
The genome-wide GC table uses non-overlapping 30 nt windows binned into five genome-wide GC quintiles. Bin boundaries are recorded with the object so that the motif frequency tables and the genome table are always binned on the same scale.
Fixes on NOTES from biocchecks
Added 4 spaces as suggested