make_biom_tables: Make biom tables (relative abundance and absolute abundance)...

In econtijoch/Biomass-Workflow: Microbial Density Data Generation and Analysis Tools

Description

Make biom tables (relative abundance and absolute abundance) from a sequencing object (individual_scale output)

Usage

make_biom_tables(sequencing_object, output_type = "biom",
  output_prefix = NULL, output_directory = getwd())

Arguments

sequencing_object	output from individual_scale that contains microbial density-scaled sequencing data
output_type	'biom' or 'phyloseq', to indicate which format to generate the resulant OTU tables in within R
output_prefix	(optional) prefix to give otu tables. By providing this, you will write .biom otu tables to your working directory or specified output directory
output_directory	(optional) specify an output directory to write otu tables in .biom format to (must provide output_prefix)

Value

a list of otu tables (relative and absolute) in the specified format. Additionally, if specified, .biom files will be written

econtijoch/Biomass-Workflow documentation built on May 15, 2019, 7:59 p.m.