uniqueSeqs: Unique sequences

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

Unique sequences

Description

Aggregates all productive sequences within a list of data frames by duplicate_count.

Usage

uniqueSeqs(productive_table = productive_table, unique_type = "junction_aa")

Arguments

productive_table	A tibble of productive amino acid sequences imported using the function LymphoSeq2 function productiveSeq() where the aggregate parameter was set to "junction_aa".
unique_type	Use "junction_aa" (the default) to aggregate by amino acid sequences. Use "junction" to aggregate by nucleotide sequences.

Value

A data frame of unique amino acid sequences from the list of data frames aggregated by "duplicate_count".

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")
unique_seqs <- LymphoSeq2::uniqueSeqs(productive_table = amino_table,
 unique_type = "junction_aa")

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