import_dada2: Import function to read the the output of dada2 as phyloseq...

In yiluheihei/microbiomeMarker: microbiome biomarker analysis toolkit

Import function to read the the output of dada2 as phyloseq object

Description

Import the output of dada2 into phyloseq object

Usage

import_dada2(
  seq_tab,
  tax_tab = NULL,
  sam_tab = NULL,
  phy_tree = NULL,
  keep_taxa_rows = TRUE
)

Arguments

seq_tab	matrix-like, ASV table, the output of dada2::removeBimeraDenovo.
tax_tab	matrix, taxonomy table, the output of dada2::assignTaxonomy or dada2::addSpecies.
sam_tab	data.frame or phyloseq::sample_data, sample data
phy_tree	ape::phylo class or character represents the path of the tree file
keep_taxa_rows	logical, whether keep taxa in rows or not in the otu_table of the returned phyloseq object, default TRUE.

Details

The output of the dada2 pipeline is a feature table of amplicon sequence variants (an ASV table): A matrix with rows corresponding to samples and columns to ASVs, in which the value of each entry is the number of times that ASV was observed in that sample. This table is analogous to the traditional OTU table. Conveniently, taxa names are saved as ASV1, ASV2, ..., in the returned phyloseq object.

Value

phyloseq::phyloseq object hold the taxonomy info, sample metadata, number of reads per ASV.

Examples

seq_tab <- readRDS(system.file("extdata", "dada2_seqtab.rds",
    package = "microbiomeMarker"
))
tax_tab <- readRDS(system.file("extdata", "dada2_taxtab.rds",
    package = "microbiomeMarker"
))
sam_tab <- read.table(system.file("extdata", "dada2_samdata.txt",
    package = "microbiomeMarker"
), sep = "\t", header = TRUE, row.names = 1)
ps <- import_dada2(seq_tab = seq_tab, tax_tab = tax_tab, sam_tab = sam_tab)
ps

yiluheihei/microbiomeMarker documentation built on Nov. 5, 2023, 7:19 a.m.