geneFreq: Gene frequencies

In elulu3/LymphoSeqTest: 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(productive_nt, locus = "V|D|J", family = FALSE)

Arguments

productive_nt	A tibble of productive sequences generated by the LymphoSeq function productiveSeq where the parameter aggregate is set to "nucleotide".
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 \ 100\

Examples

file_path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq2")

stable <- readImmunoSeq(path = file_path)

ntable <- productiveSeq(study_table = stable, aggregate = "nucleotide")

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

elulu3/LymphoSeqTest documentation built on Aug. 27, 2022, 5:47 a.m.