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

In davidcoffey/LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors

Description

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

Usage

searchPublished(list)

Arguments

list	A list of data frames generated by the LymphoSeq functions readImmunoSeq or productiveSeq. "aminoAcid", "frequencyCount", and "count" are required columns.

Value

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.

See Also

Refer to the LymphoSeqDB package for details regarding the publishedTRB database.

Examples

file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")

file.list <- readImmunoSeq(path = file.path)

productive.aa <- productiveSeq(file.list = file.list, aggregate = "aminoAcid")

searchPublished(list = productive.aa)

davidcoffey/LymphoSeq documentation built on Dec. 31, 2019, 9:52 p.m.