create_community_table_subsets: Create subsets of phyloseq objects based on ASV/OTU counts...

In RJ333/phyloseq2ML: Connects Phyloseq To Ranger And Keras

Description

This subsetting function allows to create multiple combinations of subsets from a list of phyloseq objects. The lowest taxonomic level (usually ASV or OTU) is always included, further taxonomic levels can be specified as described below. The call to 'phyloseq::tax_glom' can be slow, therefore package 'speedyseq' is used, if installed.

Usage

create_community_table_subsets(
  subset_list,
  thresholds,
  tax_ranks = NULL,
  taxa_prefix,
  ...
)

Arguments

subset_list	a list of phyloseq objects
thresholds	an integer vector specifying the input to 'filter_taxa(sum(x > threshold) >= num_samples)', will be formatted with with digits after . later string splits
tax_ranks	specifying the tax ranks to agglomerate in the form of 'setNames(c("To_genus", To_family), c("Genus", "Family"))'. Here, "To_genus" is the corresponding taxonomic level in tax_table() and "Genus" is appended to the name the agglomerated data.frame in the results list for later distinction. Check taxa rank using 'colnames(tax_table(TNT_communities))'
taxa_prefix	The leading name of your taxa, e.g. 'ASV' or 'OTU', must not contain an underscore or white space
...	further argument passed on to filter_subsets()

Value

A list of subsetted community tables for each combination of phyloseq_subset, thresholds and tax_ranks (+ ASV/OTU)

RJ333/phyloseq2ML documentation built on June 2, 2020, 9:25 p.m.