overlaps="flag" option mentioned in vignette but does not exist

[MelinaKlostermann]

The vignette states for the overlaps in the gene assignment function:
Additionally, option overlaps="flag" will just flag all overlaps with the tag ambiguous and option overlaps="remove" will remove all those cases.

However

bds_alt_gene_asignment <- assignToGenes(bds_final, 
                                        overlaps="flag",
                                        anno.genes = gns,
                                        )

Gives the error:
Error in match.arg(overlaps, choices = c("frequency", "hierarchy", "remove", :
'arg' should be one of “frequency”, “hierarchy”, “remove”, “keep”

I guess "flag" was replaced by "keep". However keep does not apply a flag as described in the vignette. We should maybe just update the vignette.