data_fungi_mini: Fungal OTU in phyloseq format

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Fungal OTU in phyloseq format

Description

It is a subset of the data_fungi dataset including only Basidiomycota with more than 5000 sequences.

Usage

data(data_fungi_mini)

data(data_fungi_mini)

Format

A physeq object containing 45 taxa with references sequences described by 14 taxonomic ranks and 137 samples described by 7 sample variables:

• X: the name of the fastq-file

• Sample_names: the names of ... the samples

• Treename: the name of an tree

• Sample_id: identifier for each sample

• Height: height of the sample in the tree

• Diameter: diameter of the trunk

• Time: time since the dead of the tree

A physeq object containing 45 taxa with references sequences described by 14 taxonomic ranks and 137 samples described by 7 sample variables:

• X: the name of the fastq-file

• Sample_names: the names of ... the samples

• Treename: the name of an tree

• Sample_id: identifier for each sample

• Height: height of the sample in the tree

• Diameter: diameter of the trunk

• Time: time since the dead of the tree

Details

Obtain using data_fungi_mini <- subset_taxa(data_fungi, Phylum == "Basidiomycota") and then data_fungi_mini <- subset_taxa_pq(data_fungi_mini, colSums(data_fungi_mini@otu_table) > 5000)

adrientaudiere/MiscMetabar documentation built on Oct. 13, 2024, 9:42 p.m.