geneFreq: Gene frequencies

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

Gene frequencies

Description

Creates a data frame of VDJ gene counts and frequencies.

Usage

geneFreq(nucleotide_table, locus = "VDJ", family = FALSE)

Arguments

nucleotide_table	A tibble of productive sequences generated by the LymphoSeq2 function productiveSeq() where the parameter aggregate is set to "junction".
locus	A character vector indicating which VDJ genes to include in the output. Available options include "VDJ", "DJ", "VJ", "DJ", "V", "D", or "J".
family	A Boolean value indicating whether or not family names instead of gene names are used. If TRUE, then family names are used and if FALSE, gene names are used.

Value

Returns a data frame with the repertoire_id names, VDJ gene name, duplicate_count, and \ frequency should add to 100\

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)
nucleotide_table <- LymphoSeq2::productiveSeq(
  study_table = study_table,
  aggregate = "junction"
)
LymphoSeq2::geneFreq(nucleotide_table, locus = "VDJ", family = FALSE)

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