individual_scale: Function to process 16S sequencing data and scale individual...

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

Description

Function to process 16S sequencing data and scale individual samples by microbial density, generating absolute abundances

Usage

individual_scale(biom_file, metadata_file, taxonomy_file, filter)

Arguments

biom_file	.biom table in rhdf5 format. It is wise to use a pre-filtered table (for example, de-duplicated)
metadata_file	the mapping file used in QIIME to split your sequencing library (must include microbial density data)
taxonomy_file	a file containing taxonomy (e.g. output from assign_taxonomy.py in QIIME, or greengenes taxonomy)
filter	OPTIONAL: minimum relative abundance to filter from data

Value

a list containing OTU tables with and without taxonomy (at each given depth), both scaled and unscaled (the output is a list of lists).

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