filter_data: This function loads the raw ABRP data (as a phyloseq object)...
In kimberlyroche/rulesoflife:

filter_data

R Documentation

This function loads the raw ABRP data (as a phyloseq object) and 1) filters to a set of best-sampled hosts, 2) agglomerates taxa to the level specified, and 3) merges taxa below a specified minimum abundance across hosts

Description

This function loads the raw ABRP data (as a phyloseq object) and 1) filters to a set of best-sampled hosts, 2) agglomerates taxa to the level specified, and 3) merges taxa below a specified minimum abundance across hosts

Usage

filter_data(
  tax_level = "ASV",
  host_sample_min = 75,
  count_threshold = 1,
  sample_threshold = 0.2,
  seq_similarity_threshold = 0.99
)

Arguments

`tax_level`	taxonomic level at which to agglomerate data
`host_sample_min`	minimum sample number for host inclusion in the filtered data set
`count_threshold`	minimum count for taxon inclusion in the filtered data set
`sample_threshold`	minimum proportion of samples within each host at which a taxon must be observed at or above count_threshold

Details

Together count_threshold and sample_threshold specify a minimum representation for a taxon. Taxa below this threshold will be grouped together into an <NA> category.