Filter specific genes from the Giotto object

[IgLab-UNAV]

Sorry for such a basic question, but I've been searching through all the functions and also in this site, and I haven´t found an answer to this. How can I remove features (that from the object once it has been created? I have tried doing it in the @feat_metadata[["cell"]][["rna"]]@metaDT slot, but that doesn´t seem to update @expression$cell$rna$raw@exprMat. I can remove them from the latter, but that will leave the former unaltered. Do I have to change both and that will be enough? Is there a more clean method to do it? Cheers,

[RubD]

Not sure what you're trying to do without a reproducible example but subsetGiotto should work for you. You just need to specify which features (e.g. genes) you want to keep.

[IgLab-UNAV]

OK, that sounds reasonable, albeit somewhat counterintuite. It works with subsetGiotto(object, feat_ids = keep), where keep is the list of all gene names in the object except for those i want to remove (even if it is only one or two!). Thanks a lot,