otu_clustering: Clusters Species By Sequence Similarity

In jgmv/comecol: Community Ecology Analysis

Clusters Species By Sequence Similarity

Description

Clusters species in a community data object into Operational Taxonomy Units (OTUs) by sequence similariy.

Usage

otu_clustering(
  com,
  thr = 97,
  method = "cd-hit",
  folder = "OTU_clustering",
  cleanup_files = F,
  file = NULL,
  use_saved = F
)

Arguments

com	a community data object.
thr	threshold of sequence similarity for OTU clustering. In percentage.
method	method of clustering, either 'cd-hit' or 'blastclust'
file	the name of the file where the data will be stored as 'RData' object.
use_saved	read data from 'file' instead of importing them from scratch.

Details

The function still depends of an external bash script ('otu_clustering.sh'), whcih makes portability problematic. Future changes will aim at solving this problem.

Value

A list with community data.

Examples

otu_clustering()

jgmv/comecol documentation built on June 6, 2023, 4:07 p.m.