TopDAClonotypes: Extract top differentially abundant CDR3 sequences

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

Extract top differentially abundant CDR3 sequences

Description

This function extracts condition associated CDR3s given the result of the runDaAnalysis function with a given q-value and p-value cutoff

Usage

TopDAClonotypes(candidateList, enriched = T, pValueCutoff = 0.05,
  qvalue = 0.05)

Arguments

candidateList	the list of candidate DA CDR3s, the return value of runDaAnalysis function
enriched	logical; true returns differentially enriched CDR3s, false returns differentially de-enriched CDR3s. Default is true
pValueCutoff	the cutoff p-value, default is 0.05
qvalue	the cutoff q-value to use, default is 0.05

Value

function returns a data frame of the candidate CDR3s that have significant q-values with p-values below the pValueCutoff

Examples

TopDAClonotypes(results,enriched=T,pValueCutoff=0.05,qvalue=0.05) # results is an object holding the result of running runDaAnalysis

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