ImportDada2: Import function to load the feature table and taxonomy table...

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

Import function to load the feature table and taxonomy table of dada2

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, ...)

mp_import_dada2(seqtab, taxatab = NULL, reftree = NULL, sampleda = NULL, ...)

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, treedata or character, the treedata or 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.
...	additional parameters.

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")
mpse <- mp_import_dada2(seqtab=seqtab, taxatab=taxa,
                   sampleda=sampleda)
mpse

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