VDJ_db_annotate: Wrapper function of VDJ_antigen_integrate function

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Wrapper function of VDJ_antigen_integrate function

Description

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).

Usage

VDJ_db_annotate(VDJ, db.list, database.features, match, homology, lv.distance)

Arguments

VDJ	VDJ or VDJ.GEX.matrix[[1]] object, as obtained from the VDJ_GEX_matrix function in Platypus.
db.list	list of database dataframes or csv file paths, obtained from VDJ_db_load with .
database.features	list of features/column names to be integrated from the databases.
match	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').
homology	string - 'exact' for exact sequence matchings, 'homology' for homology matching.
lv.distance	integer - maximum Levehnstein distance threshold for the homology matchings.

Value

VDJ with new columns - antigen information integrated from the antigen databases.

Examples

try({
VDJ_db_annotate(VDJ=VDJ,db.list=db.list,database.features='Epitope',match='cdr3.aa',homology=FALSE)
})

Platypus documentation built on Oct. 18, 2024, 5:08 p.m.