Alternative to newBASiCS_Data?

[catavallejos]

The newBASiCS_Data is legacy from the pre-SingleCellExperiment world. Probably good to create a new function that directly updates a SingleCellExperiment object to add spike-in information and/or batch info. Here is a prototype

myFun <- function(SCE, BatchInfo = NULL, SpikeInput = NULL) {
     colData(SCE)$BatchInfo <- BatchInfo
     metadata(SCE)$SpikeInput <- SpikeInput
     return(SCE)
}

The prototype above could be extended to add spike-in counts as altExp.

[catavallejos]

@alanocallaghan if you agree with this change, I'd remove newBASiCS_Data from the workflow as it may be eventually deprecated. Instead, I'd just update the existent SingleCellExperiment objects

[alanocallaghan]

Yeah as noted in #133 it's a bit clunky, I'd maybe remove it from the workflow as it currently requires you to work around the implementation of SCE objects

[catavallejos]

Thanks! Yes, I forgot about #133 - thanks for the reminder! I am going through that section in the workflow, so I will remove the use of newBASiCS_Data

[alanocallaghan]

I think it should be deprecated for next release. Also a note, when changing it we should probably also store the spike-in concentrations in rowdata of altExp, since it ensures matching identifiers etc (#169)

[catavallejos]

I agree, that’s a much more elegant way to add the spike in info

[alanocallaghan]

Great! I'll make a kanban project for 3.12 to note the issues we can try to get done by next release

[catavallejos]

Yes please! I am becoming a big fan of kanban projects 😄