build_tree: building tree

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

building tree

Description

The function can be used to building tree.

Usage

build_tree(seqs, ...)

## S4 method for signature 'DNAStringSet'
build_tree(seqs, ...)

## S4 method for signature 'DNAbin'
build_tree(seqs, ...)

## S4 method for signature 'character'
build_tree(seqs, ...)

Arguments

seqs	DNAStringSet or DNAbin, the object of R.
...	additional parameters, see also AlignSeqs.

Value

the phylo class of tree.

Author(s)

Shuangbin Xu

Examples

## Not run: 
    seqtabfile <- system.file("extdata", "seqtab.nochim.rds", 
                              package="MicrobiotaProcess")
    seqtab <- readRDS(seqtabfile)
    refseq <- colnames(seqtab)
    names(refseq) <- paste0("OTU_",seq_len(length(refseq)))
    refseq <- Biostrings::DNAStringSet(refseq)
    tree <- build_tree(refseq)
    or
    tree <- build_tree(refseq) 

## End(Not run)

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.