klustering: KTU clustering

In poyuliu/KTU: “KTU” (K-mer Taxonomic Unit) algorithm improves biological relevance in microbiome associated study

KTU clustering

Description

K-mer taxonomic unit clustering

Usage

klustering(
  repseq,
  pscore = FALSE,
  feature.table = NULL,
  write.fasta = TRUE,
  step = c(5, 10),
  search.min = NULL,
  search.max = NULL,
  cores = 1
)

Arguments

repseq	The fasta file path
pscore	pscore=TRUE/FLASE: using k-mer present scores (tetranucleotide features 0:absent; 1:present in one direction; 2:present in both direction of a sequence)/k-mer frequency
feature.table	(optional) 'data.frame' formated ASV/OTU table
write.fasta	(optional) write out a representative KTU sequence fasta file
step	Split searching range for optimal K. Two step searching process: large scale searching in the first round and smaller scale searching in the second round. Default is 'step=c(5,10)'.
search.min	The minimum K for searching, default is 'NULL' = tip numbers at 0.03 height of cosine hierarchical clustering tree
search.max	The maximum K for searching, default is 'NULL' = tip numbers at 0.015 height of cosine hierarchical clustering tree
cores	Numbers of CPUs

Value

KTU.table Aggregated KTU table

ReqSeq Representative KTU sequences

kmer.table Tetranucleotide present score table or tetranucleotide frequency table

clusters K-clusters of input features

poyuliu/KTU documentation built on May 23, 2022, 11:06 a.m.