qSIP_atom_excess_format_MAGs

Reformat a phyloseq object of qSIP_atom_excess_MAGs analysis

Statistical analysis as part of a quantitative stable isotope
probing (SIP) metagenomics study to identify isotope incorporating
metagenomic features. Helpful reading and a vignette in bookdown
format is provided on the package site
<https://zielslab.github.io/SIPmg.github.io/>.

Pranav Sampara

SIPmg

Statistical Analysis to Identify Isotope Incorporating
Metagenomic Features

Kate Waring

Ryan Ziels

Alma Garcia Roche

qSIP_atom_excess_format_MAGs function

<dl><dt>physeq</dt>
<dd>A phyloseq object</dd>
<dt>control_expr</dt>
<dd>An expression for identifying unlabeled control
samples in the phyloseq object (eg., "Substrate=='12C-Con'")</dd>
<dt>treatment_rep</dt>
<dd>Which column in the phyloseq sample data designates
replicate treatments</dd></dl>

Arguments

Reformat a phyloseq object of qSIP_atom_excess_MAGs analysis — qSIP_atom_excess_format_MAGs

<dl>

<dt>physeq</dt>
<dd>A phyloseq object</dd>


<dt>control_expr</dt>
<dd>An expression for identifying unlabeled control
samples in the phyloseq object (eg., "Substrate=='12C-Con'")</dd>


<dt>treatment_rep</dt>
<dd>Which column in the phyloseq sample data designates
replicate treatments</dd>

</dl>

qSIP_atom_excess_format_MAGs: Reformat a phyloseq object of qSIP_atom_excess_MAGs analysis

Description

Usage

Value

Arguments