relative_abd_without_specific_sample: Compute taxa/OTU abundance relative to the total dataset

In cpauvert/psadd: Additions to phyloseq package for microbiome analysis

Description

Convenience function to divide taxa_sums output vector by the total number of sequences. Samples present in the second phyloseq object –specific– are discarded from the first one –physeq. Taxa/OTU present in the second phyloseq object –specific– and supposedly of interest are stored. The relative abundances of these taxa/OTU of interest are then computed.

Usage

relative_abd_without_specific_sample(physeq, specific)

Arguments

physeq	otu_table-class, or phyloseq-class
specific	otu_table-class, or phyloseq-class containing samples of interest to examine (e.g. Negative or Positive Controls).

Value

A numeric-class with length equal to the number of species present in the second –specific– phyloseq object. Names indicate the taxa ID, and value equal to the taxa/OTU relative abundance in the first –physeq– object (pruned of specific samples).

See Also

taxa_sums on which this function is based. See ctrl_samples_stats for a usage example.

cpauvert/psadd documentation built on Nov. 22, 2020, 9:19 a.m.