List top neoantigens for each sample and/or by clones within each sample.

garnish_antigens(dt, nhits = 2, binding_cutoff = 500)

Arguments

dt

An output data table from garnish_affinity, either a data table object or path to a file.

nhits

Integer. Maximum number of prioritized neoantigens per clone to return, default is 2.

binding_cutoff

Numeric. Affinity threshold in nM to consider neoantigens, default is 500.

Value

A data table with the top neoantigen per sample, and if possible per clone, in rank order of clone frequency. Neoantigens are prioritized by permissive dissimilarity and iedb_score thresholds and then by differential agretopicity.

See also