searchPublished: Search for T cell receptor beta CDR3 amino acid sequences...

In shashidhar22/LymphoSeq2: Analyze high-throughput sequencing of T and B cell receptors

Search for T cell receptor beta CDR3 amino acid sequences with known antigen specificity

Description

Search for published T cell receptor beta CDR3 amino acid sequences with known antigen specificity in a list of data frames.

Usage

searchPublished(study_table)

Arguments

study_table

A tibble generated by the LymphoSeq2 functions readImmunoSeq() or productiveSeq(). "junction_aa", "duplicate_frequency", and "duplicate_count" are required columns.

Value

Returns a tibble with each instance that a 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.

Examples

file_path <- system.file("extdata", "TCRB_sequencing",
 package = "LymphoSeq2")
study_table <- LymphoSeq2::readImmunoSeq(path = file_path, threads = 1)
study_table <- LymphoSeq2::topSeqs(study_table, top = 100)
amino_table <- LymphoSeq2::productiveSeq(study_table = study_table,
 aggregate = "junction_aa")
LymphoSeq2::searchPublished(amino_table)

shashidhar22/LymphoSeq2 documentation built on Jan. 16, 2024, 4:29 a.m.