sequencing_analysis_wrapper: Sequencing Analysis Wrapper

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

Description

Sequencing Analysis Wrapper

Usage

sequencing_analysis_wrapper(biom_file, metadata_file, taxonomy_file, tree_file,
  method = "PCoA", distance = "unifrac", n_axes = 10)

Arguments

biom_file	otu table in biom format
metadata_file	mapping file (QIIME-ready)
taxonomy_file	file that contains taxonomy (e.g. greengenes)
tree_file	taxonomic tree information (e.g. greengenes)
method	dimensionality reduction method (e.g. PCoA, NMDS, DCA)
distance	distance metric to use (e.g. unifrac, bray, jaccard)
n_axes	number of axes to get from PCoA

Value

list containing individual components of analyzed data ready for plotting, etc.

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