Wraps the VDJ_antigen_integrate function and uses it to annotate a VDJ dataframe with antigen information. Needs to VDJ_db_load to be executed first, with preprocess=T and vgm.names=T to obtain the same column names as in the VDJ (to allow for sequence matching).
VDJ_db_annotate(VDJ, db.list, database.features, match, homology, lv.distance)VDJ or VDJ.GEX.matrix[[1]] object, as obtained from the VDJ_GEX_matrix function in Platypus.
list of database dataframes or csv file paths, obtained from VDJ_db_load with .
list of features/column names to be integrated from the databases.
string - sequences by which to match and integrate the antigen information. Currently, only 'cdr3.aa' and 'cdrh3.aa' are supported, as all databases have these two sequence types ('VJ_cdr3s_aa','VDJ_cdr3s_aa').
string - 'exact' for exact sequence matchings, 'homology' for homology matching.
integer - maximum Levehnstein distance threshold for the homology matchings.
VDJ with new columns - antigen information integrated from the antigen databases.
if (FALSE) {
VDJ_db_annotate(VDJ=VDJ,db.list=db.list,database.features='Epitope',match='cdr3.aa',homology=FALSE)
}