import_dada2: Import function to load the feature table and taxanomy table...

In MicrobiotaProcess: an R package for analysis, visualization and biomarker discovery of microbiome

Description

the function can import the ouput of dada2, and generated the phyloseq obj contained the argument class.

Usage

import_dada2(
  seqtab,
  taxatab = NULL,
  reftree = NULL,
  sampleda = NULL,
  btree = FALSE,
  ...
)

Arguments

seqtab	matrix, feature table, the output of removeBimeraDenovo.
taxatab	matrix, a taxonomic table, the output of assignTaxonomy, or the ouput of addSpecies.
reftree	phylo or character, the phylo class of tree, or the tree file.
sampleda	data.frame or character, the data.frame of sample information, or the file of sample information, nrow samples X ncol factors.
btree	logical, whether building the tree, default is FALSE.
...,	additional parameters, see also build_tree.

Value

phyloseq class contained the argument class.

Author(s)

Shuangbin Xu

Examples

seqtabfile <- system.file("extdata", "seqtab.nochim.rds",
                          package="MicrobiotaProcess")
taxafile <- system.file("extdata", "taxa_tab.rds",
                        package="MicrobiotaProcess")
seqtab <- readRDS(seqtabfile)
taxa <- readRDS(taxafile)
sampleda <- system.file("extdata", "mouse.time.dada2.txt", 
                        package="MicrobiotaProcess")
ps <- import_dada2(seqtab=seqtab, taxatab=taxa,
                   sampleda=sampleda)
ps

MicrobiotaProcess documentation built on April 18, 2021, 6 p.m.