searchDB: 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 from IEDB, VdjDB and McPASDb

Description

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

Usage

searchDB(study_table, dbname = "all", chain = "trb")

Arguments

study_table	A tibble generated by the LymphoSeq2 functions readImmunoSeq(), productiveSeq(), searchPublished() or topSeqs(). "junction_aa", "duplicate_frequency", and "duplicate_count" are required columns.
dbname	A vector of database source to search for the antigenic specificity of a T-cell or B-cell in the dataset: "all", "IEDB", "McPAS-TCR", "VdjDB".
chain	The receptor chain type to search in the public databases: "tra", "trb", "light", "heavy".

Value

Returns the input table annotated with the any recorded antigenic specificity from the public databases.

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")
top_seqs <- LymphoSeq2::topSeqs(productive_table = amino_table, top = 1)
LymphoSeq2::searchDB(study_table = top_seqs, dbname = "all", chain = "trb")

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