subset_taxa_tax_control: Subset taxa using a taxa control or distribution based method

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Subset taxa using a taxa control or distribution based method

Description

There is 3 main methods : discard taxa (i) using a control taxa (e.g. truffle root tips), (ii) using a mixture models to detect bimodality in pseudo-abundance distribution or (iii) using a minimum difference threshold pseudo-abundance. Each cutoff is defined at the sample level.

Usage

subset_taxa_tax_control(
  physeq,
  taxa_distri,
  method = "mean",
  min_diff_for_cutoff = NULL
)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
taxa_distri	(required) a vector of length equal to the number of samples with the number of sequences per sample for the taxa control
method	(default: "mean") a method to calculate the cut-off value. There are 6 available methods: cutoff_seq: discard taxa with less than the number of sequence than taxa control, cutoff_mixt: using mixture models, cutoff_diff: using a minimum difference threshold (need the argument min_diff_for_cutoff) min: the minimum of the three firsts methods max: the maximum of the three firsts methods mean: the mean of the three firsts methods
min_diff_for_cutoff	(int) argument for method cutoff_diff. Required if method is cutoff_diff, min, max or mean

Value

A new phyloseq-class object.

Author(s)

Adrien Taudière

Examples

subset_taxa_tax_control(data_fungi,
  as.numeric(data_fungi@otu_table[, 300]),
  min_diff_for_cutoff = 2
)

MiscMetabar documentation built on Oct. 8, 2024, 1:07 a.m.