filter_taxa {OTUtable}

Filter Taxa Based on Abundance and Persistence

Description

Returns a table containing only taxa that meet the imposed requirements of a minimum abundance and a minimum number of samples containing that taxon

Usage

filter_taxa(table, abundance, persistence)

Arguments

table

A table containing the relative abundances of each OTU or taxon in the form produced by clean_shared(). Can be used on the output of grab_groups() or combine_otus()

abundance

The minimum threshold for percentage of reads attributed to a taxon in at least one sample. Taxa at abundances greater than or equal this number will be retained.

persistence

The minimum threshold for the percentage of samples in which a taxon has been observed. Taxa at abundances greater than or equal this number will be retained.

Value

Returns a table with all taxa that met the imposed thresholds

Note

Thanks Juliana Dias for suggesting this function!

Author(s)

Alexandra Linz <[e-mail]>

Examples

# To make a table containing only OTUs with at least 0.1% abundance 
# in at least one sample that were observed 
# (at any abundance) in at least 50% of samples:
# library(OTUtable)
# data(otu_table)
# filtered_table <- filter_taxa(otu_table, abundance = 0.1, persistence = 50)

# To make a table containing only phyla with at least 10% abundance 
# in any one sample and were observed 
# at any abundance in at least 10% of samples:
# data(taxonomy)
# phylum_table <- combine_otus("Phylum", otu_table, taxonomy)
# filtered_phylum_table <- filter_taxa(phylum_table, abundance = 10, persistence = 10)