The inner workings of fdge() needs to be refactored so that the biocbiox() creation
is separated into more discrete steps that just use the facile api.
The current biocbox creation is tied to the fdge_method and filtering strategy in some
type of monolithic way that needs to be pulled apart so that supplying a
FacileBiocData::FacileBiocDataStore object works more seamlessly.
The fdge() steps should be broken down into these steps:
[ ] Instantiation of the correct bioconductor data container given the dge_method
[ ] Downstream filtering based on the design, using a new public S3 method
filter_by_feature_abundance, a facile wrapper to edgeR::filterByExpr() (#24)
[ ] An inner helper to fdge would then be responsible for executing the dge_method, ie.
that should then take an input DGEList and then voom it, if dge_method == "voom"
The inner workings of
fdge()needs to be refactored so that thebiocbiox()creation is separated into more discrete steps that just use the facile api.The current biocbox creation is tied to the fdge_method and filtering strategy in some type of monolithic way that needs to be pulled apart so that supplying a
FacileBiocData::FacileBiocDataStoreobject works more seamlessly.The fdge() steps should be broken down into these steps:
dge_methodfilter_by_feature_abundance, a facile wrapper toedgeR::filterByExpr()(#24)fdgewould then be responsible for executing thedge_method, ie. that should then take an input DGEList and then voom it, ifdge_method == "voom"