computeVgeneEnrichement: V-gene usage analysis in differentially abundant CDR3s

In dyohanne/RepAn: Differential abundance Analysis for deep sequenced immune repertoire (Repseq) datasets

V-gene usage analysis in differentially abundant CDR3s

Description

This function compares observed V-gene frequencies to frequencies obtained from randomly sampled sets of CDR3s from pooled repertoires of all samples to evaluate bias in V-gene usage

Usage

computeVgeneEnrichement(repSamObj, DaClonotypes, n = 20)

Arguments

repSamObj	is a repseq data object containing all repertoire sample data
DaClonotypes	a vector of CDR3 amino acid sequences that are considered to be differentially abundant
n	the number of repeat resamples to perform; each random resample samples CDR3s the same size as the DaClonotypes. Default is 20

Value

function returns a data frame with the observed frequency, frequencies in random resamples, mean of the frequencies in the random resamples, the p-value estimated from the null distribution of resampled frequencies, and percent increase in v-gene usage for every V-genes used in the DA DR3s

dyohanne/RepAn documentation built on Feb. 3, 2023, 2:41 p.m.