getClusterLables: This function performs pairwise 4-mer nt usage clustering of...

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

This function performs pairwise 4-mer nt usage clustering of clonotypes in repSeq data

Description

This function performs pairwise 4-mer nt usage clustering of clonotypes in repSeq data

Usage

getClusterLables(sam, k = 10, clusterby = "NT", kmerWidth = 4,
  posWt = F, distMethod = "euclidean", useDynamicTreeCut = T,
  hcmethod = "complete")

Arguments

sam	a repertoire data (of only productive clonotypes,immunoseq format) for whose clonotypes are going to be clustered based on 4-mer usage frequencies.

Value

a list containing the clonotypes,clonotypes with 4-mer usage frequencies,distance matrix between clonotypes,cluster labels for each clonotype,and cluster centroids.

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