Search for T cell receptor beta CDR3 amino acid sequences with known antigen specificity
Search for published T cell receptor beta CDR3 amino acid sequences with known antigen specificity in a list of data frames.
A list of data frames generated by the LymphoSeq functions readImmunoSeq or productiveSeq. "aminoAcid", "frequencyCount", and "count" are required columns.
Returns a data frame of each sample name and instance in the sample that the published TCR sequence appeared along with additional information including antigen specificity, epitope, HLA type, and PubMed ID (PMID) for the reference where the sequence was characterized. The publishedTRB database is located in a separate package called LymphoSeqDB that should be loaded automatically.
Refer to the LymphoSeqDB package for details regarding the publishedTRB database.
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